diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 48fbb4b6b1..bd10494805 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -256,6 +256,10 @@ jobs:
- tags: "tabix/tabix"
- tags: "tiddit/sv"
- tags: "untar"
+ - tags: "pipeline_sarek"
+ include:
+ - tags: "pipeline_sarek"
+ profile: "test,docker"
env:
NXF_ANSI_LOG: false
TEST_DATA_BASE: "${{ github.workspace }}/test-datasets"
diff --git a/.github/workflows/cloudtest.yml b/.github/workflows/cloudtest.yml
index 829d870ff5..546634c42e 100644
--- a/.github/workflows/cloudtest.yml
+++ b/.github/workflows/cloudtest.yml
@@ -31,79 +31,76 @@ on:
default: true
jobs:
- trigger-profile-test:
- name: Run AWS tests
+ trigger-test:
+ name: launch
runs-on: ubuntu-latest
+ if: ${{ github.repository == 'nf-core/sarek' }}
strategy:
fail-fast: false
matrix:
include:
- profile: test_aws
- enabled: ${{ ( github.repository == 'nf-core/sarek' ) && ( github.event_name != 'workflow_dispatch' || ( inputs.test && inputs.aws ) ) }}
+ test: test
+ cloud: aws
+ compute_env: TOWER_COMPUTE_ENV
+ workdir: TOWER_BUCKET_AWS
- profile: test_azure
- enabled: ${{ ( github.repository == 'nf-core/sarek' ) && ( github.event_name != 'workflow_dispatch' || ( inputs.test && inputs.azure ) ) }}
+ test: test
+ cloud: azure
+ compute_env: TOWER_CE_AZURE_CPU
+ workdir: TOWER_BUCKET_AZURE
- profile: test_full_aws
- enabled: ${{ ( github.repository == 'nf-core/sarek' ) && ( github.event_name != 'workflow_dispatch' || ( inputs.somatic && inputs.aws ) ) }}
+ test: somatic
+ cloud: aws
+ compute_env: TOWER_COMPUTE_ENV
+ workdir: TOWER_BUCKET_AWS
- profile: test_full_azure
- enabled: ${{ ( github.repository == 'nf-core/sarek' ) && ( github.event_name != 'workflow_dispatch' || ( inputs.somatic && inputs.azure ) ) }}
+ test: somatic
+ cloud: azure
+ compute_env: TOWER_CE_AZURE_CPU
+ workdir: TOWER_BUCKET_AZURE
- profile: test_full_germline_aws
- enabled: ${{ ( github.repository == 'nf-core/sarek' ) && ( github.event_name != 'workflow_dispatch' || ( inputs.germline && inputs.aws ) ) }}
+ test: germline
+ cloud: aws
+ compute_env: TOWER_COMPUTE_ENV
+ workdir: TOWER_BUCKET_AWS
- profile: test_full_germline_azure
- enabled: ${{ ( github.repository == 'nf-core/sarek' ) && ( github.event_name != 'workflow_dispatch' || ( inputs.germline && inputs.azure ) ) }}
- - profile: test_full_germline_ncbench_agilent_aws
- enabled: ${{ ( github.repository == 'nf-core/sarek' ) && ( github.event_name != 'workflow_dispatch' || ( inputs.germline_ncbench_agilent && inputs.aws ) ) }}
+ test: germline
+ cloud: azure
+ compute_env: TOWER_CE_AZURE_CPU
+ workdir: TOWER_BUCKET_AZURE
+ - profile: test_full_germline_ncbench_agilent
+ test: germline_ncbench_agilent
+ cloud: aws
+ compute_env: TOWER_COMPUTE_ENV
+ workdir: TOWER_BUCKET_AWS
steps:
# Launch workflow on AWS Batch
- - name: AWS Launch
+ - name: Launch
uses: seqeralabs/action-tower-launch@v2
- if: ${{ matrix.enabled && ( github.event_name != 'workflow_dispatch' || inputs.aws ) }}
+ # If inputs item exists (i.e. workflow_dispatch), then we find matrix.test and check it is false
+ # If is false, we negate and run the job
+ if: ( !contains(inputs[matrix.test], 'false') && !contains(inputs[matrix.cloud], 'false') )
with:
run_name: sarek_${{ matrix.profile }}
workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
- compute_env: ${{ secrets.TOWER_COMPUTE_ENV }}
+ compute_env: ${{ secrets[matrix.compute_env] }}
revision: ${{ github.sha }}
- workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/sarek/work-${{ github.sha }}/${{ matrix.profile }}
+ workdir: ${{ secrets[matrix.workdir] }}/work/sarek/work-${{ github.sha }}/${{ matrix.profile }}
parameters: |
{
"hook_url": "${{ secrets.MEGATESTS_ALERTS_SLACK_HOOK_URL }}",
- "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/sarek/results-${{ github.sha }}/${{ matrix.profile }}/"
+ "outdir": "${{ secrets[matrix.workdir] }}/sarek/results-${{ github.sha }}/${{ matrix.profile }}/"
}
profiles: ${{ matrix.profile }}
- uses: actions/upload-artifact@v3
- name: Save AWS Logs
+ name: Save Logs
if: success() || failure()
with:
- name: tower-aws-${{ matrix.profile }}-log
- path: |
- tower_action_*.log
- tower_action_*.json
-
- # Launch workflow using Tower CLI tool action
- - name: Azure Launch
- uses: seqeralabs/action-tower-launch@v2
- if: ${{ matrix.enabled && ( github.event_name != 'workflow_dispatch' || inputs.azure ) }}
- with:
- run_name: sarek_${{ matrix.profile }}
- workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
- access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
- compute_env: ${{ secrets.TOWER_CE_AZURE_CPU }}
- revision: ${{ github.sha }}
- workdir: ${{ secrets.TOWER_BUCKET_AZURE}}/sarek/work-${{ github.sha }}/${{ matrix.profile }}
- parameters: |
- {
- "hook_url": "${{ secrets.MEGATESTS_ALERTS_SLACK_HOOK_URL }}",
- "outdir": "${{ secrets.TOWER_BUCKET_AZURE }}/sarek/results-${{ github.sha }}/${{ matrix.profile }}/"
- }
- profiles: ${{ matrix.profile }}
-
- - uses: actions/upload-artifact@v3
- name: Save Azure Logs
- if: success() || failure()
- with:
- name: tower-azure-${{ matrix.profile }}-log
+ name: tower-${{ matrix.profile }}-log
path: |
tower_action_*.log
tower_action_*.json
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 7d1434d995..4257960df7 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -5,6 +5,52 @@ All notable changes to this project will be documented in this file.
The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
+## [3.4.2](https://github.com/nf-core/sarek/releases/tag/3.4.2) - Sájtáristjåhkkå
+
+Sájtáristjåhkkå is another peak (just under 2k) in the Pårte massif, it is one of the few peaks in Sweden that cannot be climbed without proper climbing equipment.
+
+### Added
+
+- [#1489](https://github.com/nf-core/sarek/pull/1489) - Added a `testdata.nf-core.sarek` key in `conf/igenomes.config` for small reference
+- [#1493](https://github.com/nf-core/sarek/pull/1493) - Added a `wave` profile
+- [#1498](https://github.com/nf-core/sarek/pull/1498) - Prepare release `3.4.2`
+
+### Changed
+
+- [#1477](https://github.com/nf-core/sarek/pull/1477) - Back to dev
+- [#1482](https://github.com/nf-core/sarek/pull/1482) - Pin `nf-prov` plugin to `1.2.2`
+- [#1485](https://github.com/nf-core/sarek/pull/1485) - Update citation for publication
+- [#1487](https://github.com/nf-core/sarek/pull/1487) - Update sentieon-modules to Sentieon `202308.02`
+- [#1490](https://github.com/nf-core/sarek/pull/1490) - Update mosdepth to `0.3.8`
+- [#1505](https://github.com/nf-core/sarek/pull/1505) - Update CITATIONS.md
+- [#1506](https://github.com/nf-core/sarek/pull/1506) - Fixing typos (`index_alignement` -> `index_alignment`)
+- [#1509](https://github.com/nf-core/sarek/pull/1509) - Update contributors
+
+### Fixed
+
+- [#1378](https://github.com/nf-core/sarek/pull/1378) - Improve cloud tests launch workflow to use matrix
+- [#1488](https://github.com/nf-core/sarek/pull/1488) - Fixing call to `GATK4_HAPLOTYPECALLER` and thereby also the test-profile `test_full_germline`
+- [#1494](https://github.com/nf-core/sarek/pull/1494) - Fix Cloud Storage objects are immutable on GCP [#1491](https://github.com/nf-core/sarek/issues/1491)
+- [#1496](https://github.com/nf-core/sarek/pull/1496) - Fix multiple DOI handling in manifest
+- [#1499](https://github.com/nf-core/sarek/pull/1499) - Remove all md5sum for mosdepth tests
+- [#1499](https://github.com/nf-core/sarek/pull/1499) - Add mosdepth dependency to all tests runnning it
+- [#1501](https://github.com/nf-core/sarek/pull/1501) - Remove string "None" param option from ascat_genome
+
+### Removed
+
+- [#1489](https://github.com/nf-core/sarek/pull/1489) - Remove `test_cache` profile
+
+### Dependencies
+
+| Dependency | Old version | New version |
+| ---------- | ----------- | ----------- |
+| `mosdepth` | 0.3.6 | 0.3.8 |
+| `sentieon` | 202308.01 | 202308.02 |
+
+### Modules / Subworkflows
+
+### Parameters
+
## [3.4.1](https://github.com/nf-core/sarek/releases/tag/3.4.1) - Balgattjåhkkå
Balgattjåhkkå is the other top peak (over 2k m) in the Pårte massif, the other one being Pårtetjåkko (Bårddetjåhkkå).
@@ -71,16 +117,16 @@ Balgattjåhkkå is the other top peak (over 2k m) in the Pårte massif, the othe
### Dependencies
-| Dependency | Old version | New version |
-| ---------- | ----------- | ----------- |
-| bcftools | 1.17 | 1.18 |
-| ensemblvep | 110.0 | 111.0 |
-| fgbio | 2.0.2 | 2.1.0 |
-| gatk | 4.4.0.0 | 4.5.0.0 |
-| gatk-spark | 4.4.0.0 | 4.5.0.0 |
-| mosdepth | 0.3.3 | 0.3.6 |
-| multiqc | 1.17 | 1.18 |
-| samtools | 1.17 | 1.19.2 |
+| Dependency | Old version | New version |
+| ------------ | ----------- | ----------- |
+| `bcftools` | 1.17 | 1.18 |
+| `ensemblvep` | 110.0 | 111.0 |
+| `fgbio` | 2.0.2 | 2.1.0 |
+| `gatk` | 4.4.0.0 | 4.5.0.0 |
+| `gatk-spark` | 4.4.0.0 | 4.5.0.0 |
+| `mosdepth` | 0.3.3 | 0.3.6 |
+| `multiqc` | 1.17 | 1.18 |
+| `samtools` | 1.17 | 1.19.2 |
### Modules / Subworkflows
@@ -89,9 +135,9 @@ Balgattjåhkkå is the other top peak (over 2k m) in the Pårte massif, the othe
### Parameter
-| Old name | New name |
-| -------------------------- | ------------------------ |
-| bcftools_annotations_index | bcftools_annotations_tbi |
+| Old name | New name |
+| ---------------------------- | -------------------------- |
+| `bcftools_annotations_index` | `bcftools_annotations_tbi` |
## [3.4.0](https://github.com/nf-core/sarek/releases/tag/3.4.0) - Pårtetjåkko
@@ -141,8 +187,8 @@ Pårtetjåkko is a mountain in the south of the park.
| Dependency | Old version | New version |
| ---------- | ----------- | ----------- |
-| fastqc | 0.11.9 | 0.12.1 |
-| multiqc | 1.15 | 1.17 |
+| `fastqc` | 0.11.9 | 0.12.1 |
+| `multiqc` | 1.15 | 1.17 |
### Modules / Subworkflows
@@ -175,9 +221,9 @@ Ráhpajávvre is the Lule Sámi spelling of Rapaselet.
### Dependencies
-| Dependency | Old version | New version |
-| -------------------------------- | ----------- | ----------- |
-| Control-FREEC/assesssignificance | 11.6b | 11.6 |
+| Dependency | Old version | New version |
+| ---------------------------------- | ----------- | ----------- |
+| `Control-FREEC/assesssignificance` | 11.6b | 11.6 |
## [3.3.1](https://github.com/nf-core/sarek/releases/tag/3.3.1) - Biellorippjávrre
@@ -201,9 +247,9 @@ A lake near the Rapaselet delta.
### Dependencies
-| Dependency | Old version | New version |
-| ------------- | ----------- | ----------- |
-| Control-FREEC | 11.6 | 11.6b |
+| Dependency | Old version | New version |
+| --------------- | ----------- | ----------- |
+| `Control-FREEC` | 11.6 | 11.6b |
## [3.3.0](https://github.com/nf-core/sarek/releases/tag/3.3.0) - Rapaselet
@@ -320,7 +366,7 @@ Vuoinesluobbalah is a lake close to Bierikjávrre.
### Fixed
-- [#1087](https://github.com/nf-core/sarek/pull/1087) - Fix wrong default memory in GATK4_CREATESEQUENCEDICTIONARY [#1085](https://github.com/nf-core/sarek/pull/1085)
+- [#1087](https://github.com/nf-core/sarek/pull/1087) - Fix wrong default memory in `GATK4_CREATESEQUENCEDICTIONARY` [#1085](https://github.com/nf-core/sarek/pull/1085)
- [#1089](https://github.com/nf-core/sarek/pull/1089) - Remove duplicated code
- [#1093](https://github.com/nf-core/sarek/pull/1093) - Fixing Ascat by reverting meta.id in channels allele_files, loci_files, gc_file and rt_file to baseName
- [#1098](https://github.com/nf-core/sarek/pull/1098) - Fix Channel issue in Mutect2 subworkflow [#1094](https://github.com/nf-core/sarek/pull/1094)
diff --git a/CITATIONS.md b/CITATIONS.md
index 632a65b795..f72966d98c 100644
--- a/CITATIONS.md
+++ b/CITATIONS.md
@@ -70,6 +70,8 @@
- [FGBio](https://github.com/fulcrumgenomics/fgbio)
+ > doi: 10.5281/zenodo.10456900
+
- [FreeBayes](https://arxiv.org/abs/1207.3907)
> Garrison E, Marth G. Haplotype-based variant detection from short-read sequencing. arXiv preprint arXiv:1207.3907 [q-bio.GN] 2012. doi: 10.48550/arXiv.1207.3907
diff --git a/README.md b/README.md
index fc283ba454..490230d700 100644
--- a/README.md
+++ b/README.md
@@ -153,6 +153,7 @@ We thank the following people for their extensive assistance in the development
- [Johannes Alneberg](https://github.com/alneberg)
- [José Fernández Navarro](https://github.com/jfnavarro)
- [Júlia Mir Pedrol](https://github.com/mirpedrol)
+- [Ken Brewer](https://github.com/kenibrewer)
- [Lasse Westergaard Folkersen](https://github.com/lassefolkersen)
- [Lucia Conde](https://github.com/lconde-ucl)
- [Malin Larsson](https://github.com/malinlarsson)
@@ -160,6 +161,7 @@ We thank the following people for their extensive assistance in the development
- [Nick Smith](https://github.com/nickhsmith)
- [Nicolas Schcolnicov](https://github.com/nschcolnicov)
- [Nilesh Tawari](https://github.com/nilesh-tawari)
+- [Nils Homer](https://github.com/nh13)
- [Olga Botvinnik](https://github.com/olgabot)
- [Oskar Wacker](https://github.com/WackerO)
- [pallolason](https://github.com/pallolason)
@@ -169,6 +171,7 @@ We thank the following people for their extensive assistance in the development
- [Sam Minot](https://github.com/sminot)
- [Sebastian-D](https://github.com/Sebastian-D)
- [Silvia Morini](https://github.com/silviamorins)
+- [Simon Pearce](https://github.com/SPPearce)
- [Solenne Correard](https://github.com/scorreard)
- [Susanne Jodoin](https://github.com/SusiJo)
- [Szilveszter Juhos](https://github.com/szilvajuhos)
@@ -193,7 +196,7 @@ For further information or help, don't hesitate to get in touch on the [Slack `#
If you use `nf-core/sarek` for your analysis, please cite the `Sarek` article as follows:
-> Friederike Hanssen, Maxime U Garcia, Lasse Folkersen, Anders Sune Pedersen, Francesco Lescai, Susanne Jodoin, Edmund Miller, Oskar Wacker, Nicholas Smith, nf-core community, Gisela Gabernet, Sven Nahnsen **Scalable and efficient DNA sequencing analysis on different compute infrastructures aiding variant discovery** _bioRxiv_ [doi: 10.1101/2023.07.19.549462](https://doi.org/10.1101/2023.07.19.549462).
+> Friederike Hanssen, Maxime U Garcia, Lasse Folkersen, Anders Sune Pedersen, Francesco Lescai, Susanne Jodoin, Edmund Miller, Oskar Wacker, Nicholas Smith, nf-core community, Gisela Gabernet, Sven Nahnsen **Scalable and efficient DNA sequencing analysis on different compute infrastructures aiding variant discovery** _NAR Genomics and Bioinformatics_ Volume 6, Issue 2, June 2024, lqae031, [doi: 10.1093/nargab/lqae031](https://doi.org/10.1093/nargab/lqae031).
> Garcia M, Juhos S, Larsson M et al. **Sarek: A portable workflow for whole-genome sequencing analysis of germline and somatic variants [version 2; peer review: 2 approved]** _F1000Research_ 2020, 9:63 [doi: 10.12688/f1000research.16665.2](http://dx.doi.org/10.12688/f1000research.16665.2).
diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml
index 20fec4d67b..206bd82386 100644
--- a/assets/multiqc_config.yml
+++ b/assets/multiqc_config.yml
@@ -3,9 +3,9 @@ custom_logo_url: https://github.com/nf-core/sarek/
custom_logo_title: "nf-core/sarek"
report_comment: >
- This report has been generated by the nf-core/sarek
+ This report has been generated by the nf-core/sarek
analysis pipeline. For information about how to interpret these results, please see the
- documentation.
+ documentation.
report_section_order:
"nf-core-sarek-methods-description":
order: -1000
diff --git a/conf/igenomes.config b/conf/igenomes.config
index 5aa3e69805..a3f57e6d7e 100644
--- a/conf/igenomes.config
+++ b/conf/igenomes.config
@@ -320,5 +320,25 @@ params {
fasta = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Sequence/WholeGenomeFasta/genome.fa"
readme = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Annotation/README.txt"
}
+ 'testdata.nf-core.sarek' {
+ dbsnp = "${params.igenomes_base}/genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz"
+ dbsnp_tbi = "${params.igenomes_base}/genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz.tbi"
+ dbsnp_vqsr = '--resource:dbsnp,known=false,training=true,truth=false,prior=2.0 dbsnp_146.hg38.vcf.gz'
+ dict = "${params.igenomes_base}/genomics/homo_sapiens/genome/genome.dict"
+ fasta = "${params.igenomes_base}/genomics/homo_sapiens/genome/genome.fasta"
+ fasta_fai = "${params.igenomes_base}/genomics/homo_sapiens/genome/genome.fasta.fai"
+ germline_resource = "${params.igenomes_base}/genomics/homo_sapiens/genome/vcf/gnomAD.r2.1.1.vcf.gz"
+ germline_resource_tbi = "${params.igenomes_base}/genomics/homo_sapiens/genome/vcf/gnomAD.r2.1.1.vcf.gz.tbi"
+ intervals = "${params.igenomes_base}/genomics/homo_sapiens/genome/genome.interval_list"
+ known_indels = "${params.igenomes_base}/genomics/homo_sapiens/genome/vcf/mills_and_1000G.indels.vcf.gz"
+ known_indels_tbi = "${params.igenomes_base}/genomics/homo_sapiens/genome/vcf/mills_and_1000G.indels.vcf.gz.tbi"
+ known_indels_vqsr = '--resource:mills,known=false,training=true,truth=true,prior=10.0 mills_and_1000G.indels.vcf.gz'
+ ngscheckmate_bed = "${params.igenomes_base}/genomics/homo_sapiens/genome/chr21/germlineresources/SNP_GRCh38_hg38_wChr.bed"
+ snpeff_db = '105'
+ snpeff_genome = 'WBcel235'
+ vep_cache_version = '110'
+ vep_genome = 'WBcel235'
+ vep_species = 'caenorhabditis_elegans'
+ }
}
}
diff --git a/conf/test.config b/conf/test.config
index 0366015081..9dd0bca957 100644
--- a/conf/test.config
+++ b/conf/test.config
@@ -18,30 +18,22 @@ params {
max_memory = '6.5GB'
max_time = '8.h'
+ // Base directory for nf-core/modules test data
+ modules_testdata_base_path = 's3://ngi-igenomes/testdata/nf-core/modules'
+
// Input data
input = "${projectDir}/tests/csv/3.0/fastq_single.csv"
- // No AWS iGenomes
- genome = null
- igenomes_ignore = true
+ // small genome on igenomes
+ igenomes_base = 's3://ngi-igenomes/testdata/nf-core/modules'
+ genome = 'testdata.nf-core.sarek'
// Small reference genome
- bcftools_annotations = "https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/sarscov2/illumina/vcf/test2.vcf.gz"
- bcftools_annotations_tbi = "https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi"
+ bcftools_annotations = "${params.modules_testdata_base_path}/genomics/sarscov2/illumina/vcf/test2.vcf.gz"
+ bcftools_annotations_tbi = "${params.modules_testdata_base_path}/genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi"
bcftools_header_lines = "${projectDir}/tests/config/bcfann_test_header.txt"
- dbsnp = "https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz"
- fasta = "https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/genome.fasta"
- germline_resource = "https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/vcf/gnomAD.r2.1.1.vcf.gz"
- intervals = "https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/genome.interval_list"
- known_indels = "https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/vcf/mills_and_1000G.indels.vcf.gz"
- ngscheckmate_bed = "https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/chr21/germlineresources/SNP_GRCh38_hg38_wChr.bed"
snpeff_cache = null
- snpeff_db = '105'
- snpeff_genome = 'WBcel235'
vep_cache = null
- vep_cache_version = '110'
- vep_genome = 'WBcel235'
- vep_species = 'caenorhabditis_elegans'
// Sentieon
sentieon_dnascope_model = "s3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/Sentieon/SentieonDNAscopeModel1.1.model"
@@ -52,9 +44,6 @@ params {
// Ignore params that will throw warning through params validation
validationSchemaIgnoreParams = 'genomes'
-
- // Base directory for nf-core/modules test data
- modules_testdata_base_path = 's3://ngi-igenomes/testdata/nf-core/modules/'
}
process {
diff --git a/conf/test/cache.config b/conf/test/cache.config
deleted file mode 100644
index 5e5145b6bc..0000000000
--- a/conf/test/cache.config
+++ /dev/null
@@ -1,133 +0,0 @@
-/*
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
- Nextflow config file for running minimal tests
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
- Defines input files and everything required to run a fast and simple pipeline test.
-
- Use as follows:
- nextflow run nf-core/sarek -profile test,, --outdir
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-*/
-
-if (System.getenv('TEST_DATA_BASE')) {
- if ("$TEST_DATA_BASE") {
- params.test_data_base = "$TEST_DATA_BASE"
- }
-}
-
-try {
- includeConfig "https://raw.githubusercontent.com/nf-core/modules/master/tests/config/test_data.config"
-} catch (Exception e) {
- System.err.println("WARNING: Could not load nf-core/modules test data config")
-}
-
-params {
- config_profile_name = 'Test profile'
- config_profile_description = 'Minimal test dataset to check pipeline function'
-
- // Limit resources so that this can run on GitHub Actions
- max_cpus = 2
- max_memory = '6.5GB'
- max_time = '8.h'
-
- // Input data
- input = "${projectDir}/tests/csv/3.0/fastq_single.csv"
-
- // No AWS iGenomes
- genome = null
- igenomes_ignore = true
-
- // Small reference genome
- bcftools_annotations = params.test_data['sarscov2']['illumina']['test2_vcf_gz']
- bcftools_annotations_tbi = params.test_data['sarscov2']['illumina']['test2_vcf_gz_tbi']
- bcftools_header_lines = "${projectDir}/tests/config/bcfann_test_header.txt"
- dbsnp = params.test_data['homo_sapiens']['genome']['dbsnp_146_hg38_vcf_gz']
- fasta = params.test_data['homo_sapiens']['genome']['genome_fasta']
- germline_resource = params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_vcf_gz']
- intervals = params.test_data['homo_sapiens']['genome']['genome_interval_list']
- known_indels = params.test_data['homo_sapiens']['genome']['mills_and_1000g_indels_vcf_gz']
- ngscheckmate_bed = params.test_data['homo_sapiens']['genome']['ngscheckmate_bed']
- snpeff_cache = null
- snpeff_db = 105
- snpeff_genome = 'WBcel235'
- vep_cache = null
- vep_cache_version = 110
- vep_genome = 'WBcel235'
- vep_species = 'caenorhabditis_elegans'
-
- // Sentieon
- sentieon_dnascope_model = "s3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/Sentieon/SentieonDNAscopeModel1.1.model"
-
- // default params
- split_fastq = 0 // no FASTQ splitting
- tools = 'strelka' // Variant calling with Strelka
-
- // Ignore params that will throw warning through params validation
- validationSchemaIgnoreParams = 'genomes,test_data'
-}
-
-process {
- // This must contain .* in order to properly overwrite the standard config in test cases
- withName:'.*:FREEC_SOMATIC'{
- ext.args = {
- [
- "sample":[
- inputformat: "pileup",
- mateorientation: "FR"
- ],
- "general":[
- bedgraphoutput: "TRUE",
- noisydata: "TRUE",
- minexpectedgc: "0",
- readcountthreshold: "1",
- sex: meta.sex,
- window: "10",
- ],
- "control":[
- inputformat: "pileup",
- mateorientation: "FR"
- ]
- ]
- }
- }
-
- withName: '.*:MUTECT2_PAIRED'{
- //sample name from when the test data was generated
- ext.args = { "--f1r2-tar-gz ${task.ext.prefix}.f1r2.tar.gz --normal-sample normal" }
- }
-
- withName: '.*:FILTERVARIANTTRANCHES'{
- ext.args = { "--info-key CNN_1D --indel-tranche 0" }
- }
-}
-
-// Enable container engines/virtualisation envs for CI testing
-// only works when specified with the profile ENV
-// otherwise tests can be done with the regular provided profiles
-if (System.getenv('PROFILE')) {
- if ("$PROFILE" == "conda") {
- conda.createTimeout = "120 min"
- conda.enabled = true
- charliecloud.enabled = false
- docker.enabled = false
- podman.enabled = false
- shifter.enabled = false
- singularity.enabled = false
- } else if ("$PROFILE" == "docker") {
- conda.enabled = false
- docker.enabled = true
- docker.runOptions = '-u $(id -u):$(id -g)'
- charliecloud.enabled = false
- podman.enabled = false
- shifter.enabled = false
- singularity.enabled = false
- } else if ("$PROFILE" == "singularity") {
- conda.enabled = false
- singularity.autoMounts = true
- singularity.enabled = true
- charliecloud.enabled = false
- docker.enabled = false
- podman.enabled = false
- shifter.enabled = false
- }
-}
diff --git a/conf/test/targeted.config b/conf/test/targeted.config
index 80fa1759d1..8ebbdf4392 100644
--- a/conf/test/targeted.config
+++ b/conf/test/targeted.config
@@ -10,7 +10,7 @@
*/
params {
- intervals = params.test_data['homo_sapiens']['genome']['genome_multi_interval_bed']
+ intervals = "${params.modules_testdata_base_path}/genomics/homo_sapiens/genome/genome.multi_intervals.bed"
nucleotides_per_second = 20
tools = null
wes = true
diff --git a/conf/test/tools.config b/conf/test/tools.config
index a91389e27b..a749ae5ea7 100644
--- a/conf/test/tools.config
+++ b/conf/test/tools.config
@@ -11,11 +11,18 @@
params {
input = "${projectDir}/tests/csv/3.0/recalibrated.csv"
- dbsnp = params.test_data['homo_sapiens']['genome']['dbsnp_138_hg38_21_vcf_gz']
- fasta = params.test_data['homo_sapiens']['genome']['genome_21_fasta']
- germline_resource = params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_21_vcf_gz']
- intervals = params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed']
- pon = params.test_data['homo_sapiens']['genome']['mills_and_1000g_indels_21_vcf_gz']
+ genome = null
+ igenomes_ignore = true
+ dbsnp = "${params.modules_testdata_base_path}/genomics/homo_sapiens/genome/chr21/germlineresources/dbsnp_138.hg38.vcf.gz"
+ dbsnp_tbi = "${params.modules_testdata_base_path}/genomics/homo_sapiens/genome/chr21/germlineresources/dbsnp_138.hg38.vcf.gz.tbi"
+ fasta_fai = "${params.modules_testdata_base_path}/genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai"
+ fasta = "${params.modules_testdata_base_path}/genomics/homo_sapiens/genome/chr21/sequence/genome.fasta"
+ germline_resource = "${params.modules_testdata_base_path}/genomics/homo_sapiens/genome/chr21/germlineresources/gnomAD.r2.1.1.vcf.gz"
+ germline_resource_tbi = "${params.modules_testdata_base_path}/genomics/homo_sapiens/genome/chr21/germlineresources/gnomAD.r2.1.1.vcf.gz.tbi"
+ intervals = "${params.modules_testdata_base_path}/genomics/homo_sapiens/genome/chr21/sequence/multi_intervals.bed"
+ pon = "${params.modules_testdata_base_path}/genomics/homo_sapiens/genome/chr21/germlineresources/mills_and_1000G.indels.hg38.vcf.gz"
+ pon_tbi = "${params.modules_testdata_base_path}/genomics/homo_sapiens/genome/chr21/germlineresources/mills_and_1000G.indels.hg38.vcf.gz.tbi"
+ ngscheckmate_bed = "${params.modules_testdata_base_path}/genomics/homo_sapiens/genome/chr21/germlineresources/SNP_GRCh38_hg38_wChr.bed"
nucleotides_per_second = 20
step = 'variant_calling'
tools = null
diff --git a/conf/test/tools_germline.config b/conf/test/tools_germline.config
index 31cb79cd93..5b8baa1996 100644
--- a/conf/test/tools_germline.config
+++ b/conf/test/tools_germline.config
@@ -11,13 +11,20 @@
params {
input = "${projectDir}/tests/csv/3.0/recalibrated_germline.csv"
- dbsnp = params.test_data['homo_sapiens']['genome']['dbsnp_138_hg38_21_vcf_gz']
- fasta = params.test_data['homo_sapiens']['genome']['genome_21_fasta']
- intervals = params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed']
- known_indels = params.test_data['homo_sapiens']['genome']['mills_and_1000g_indels_21_vcf_gz']
+ genome = null
+ igenomes_ignore = true
+ dbsnp = "${params.modules_testdata_base_path}/genomics/homo_sapiens/genome/chr21/germlineresources/dbsnp_138.hg38.vcf.gz"
+ dbsnp_tbi = "${params.modules_testdata_base_path}/genomics/homo_sapiens/genome/chr21/germlineresources/dbsnp_138.hg38.vcf.gz.tbi"
+ fasta = "${params.modules_testdata_base_path}/genomics/homo_sapiens/genome/chr21/sequence/genome.fasta"
+ fasta_fai = "${params.modules_testdata_base_path}/genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai"
+ intervals = "${params.modules_testdata_base_path}/genomics/homo_sapiens/genome/chr21/sequence/multi_intervals.bed"
+ known_indels = "${params.modules_testdata_base_path}/genomics/homo_sapiens/genome/chr21/germlineresources/mills_and_1000G.indels.hg38.vcf.gz"
+ known_indels_tbi = "${params.modules_testdata_base_path}/genomics/homo_sapiens/genome/chr21/germlineresources/mills_and_1000G.indels.hg38.vcf.gz.tbi"
known_indels_vqsr = "--resource:1000G,known=false,training=true,truth=true,prior=10.0 mills_and_1000G.indels.hg38.vcf.gz"
- known_snps = params.test_data['homo_sapiens']['genome']['hapmap_3_3_hg38_21_vcf_gz']
+ known_snps = "${params.modules_testdata_base_path}/genomics/homo_sapiens/genome/chr21/germlineresources/hapmap_3.3.hg38.vcf.gz"
+ known_snps_tbi = "${params.modules_testdata_base_path}/genomics/homo_sapiens/genome/chr21/germlineresources/hapmap_3.3.hg38.vcf.gz.tbi"
known_snps_vqsr = "--resource:hapmap,known=false,training=true,truth=true,prior=10.0 hapmap_3.3.hg38.vcf.gz"
+ ngscheckmate_bed = "${params.modules_testdata_base_path}/genomics/homo_sapiens/genome/chr21/germlineresources/SNP_GRCh38_hg38_wChr.bed"
nucleotides_per_second = 20
step = 'variant_calling'
tools = null
diff --git a/conf/test/tools_somatic.config b/conf/test/tools_somatic.config
index 93d4df8c19..2fdff58e16 100644
--- a/conf/test/tools_somatic.config
+++ b/conf/test/tools_somatic.config
@@ -11,12 +11,19 @@
params {
input = "${projectDir}/tests/csv/3.0/recalibrated_somatic.csv"
- chr_dir = params.test_data['homo_sapiens']['genome']['genome_21_chromosomes_dir']
- dbsnp = params.test_data['homo_sapiens']['genome']['dbsnp_138_hg38_21_vcf_gz']
- fasta = params.test_data['homo_sapiens']['genome']['genome_21_fasta']
- germline_resource = params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_21_vcf_gz']
- intervals = params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed']
- pon = params.test_data['homo_sapiens']['genome']['mills_and_1000g_indels_21_vcf_gz']
+ genome = null
+ igenomes_ignore = true
+ chr_dir = "${params.modules_testdata_base_path}/genomics/homo_sapiens/genome/chr21/sequence/chromosomes.tar.gz"
+ dbsnp = "${params.modules_testdata_base_path}/genomics/homo_sapiens/genome/chr21/germlineresources/dbsnp_138.hg38.vcf.gz"
+ dbsnp_tbi = "${params.modules_testdata_base_path}/genomics/homo_sapiens/genome/chr21/germlineresources/dbsnp_138.hg38.vcf.gz.tbi"
+ fasta = "${params.modules_testdata_base_path}/genomics/homo_sapiens/genome/chr21/sequence/genome.fasta"
+ fasta_fai = "${params.modules_testdata_base_path}/genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai"
+ germline_resource = "${params.modules_testdata_base_path}/genomics/homo_sapiens/genome/chr21/germlineresources/gnomAD.r2.1.1.vcf.gz"
+ germline_resource_tbi = "${params.modules_testdata_base_path}/genomics/homo_sapiens/genome/chr21/germlineresources/gnomAD.r2.1.1.vcf.gz.tbi"
+ intervals = "${params.modules_testdata_base_path}/genomics/homo_sapiens/genome/chr21/sequence/multi_intervals.bed"
+ pon = "${params.modules_testdata_base_path}/genomics/homo_sapiens/genome/chr21/germlineresources/mills_and_1000G.indels.hg38.vcf.gz"
+ pon_tbi = "${params.modules_testdata_base_path}/genomics/homo_sapiens/genome/chr21/germlineresources/mills_and_1000G.indels.hg38.vcf.gz.tbi"
+ ngscheckmate_bed = "${params.modules_testdata_base_path}/genomics/homo_sapiens/genome/chr21/germlineresources/SNP_GRCh38_hg38_wChr.bed"
nucleotides_per_second = 20
step = 'variant_calling'
tools = null
diff --git a/conf/test/tools_somatic_ascat.config b/conf/test/tools_somatic_ascat.config
index 3f37bd4b3f..ec6df8e483 100644
--- a/conf/test/tools_somatic_ascat.config
+++ b/conf/test/tools_somatic_ascat.config
@@ -10,15 +10,15 @@
*/
params {
- input = "${projectDir}/tests/csv/3.0/ascat_somatic.csv"
- genome = 'GATK.GRCh37'
- igenomes_ignore = false
- ascat_loci = "G1000_loci_hg19.zip"
- ascat_min_base_qual = 30
- chr_dir = params.test_data['homo_sapiens']['genome']['genome_21_chromosomes_dir']
- germline_resource = params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_21_vcf_gz']
- intervals = params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed']
- step = 'variant_calling'
- tools = 'ascat'
- wes = false
+ input = "${projectDir}/tests/csv/3.0/ascat_somatic.csv"
+ genome = 'GATK.GRCh37'
+ germline_resource_tbi = "${params.modules_testdata_base_path}/genomics/homo_sapiens/genome/chr21/germlineresources/gnomAD.r2.1.1.vcf.gz.tbi"
+ ascat_loci = "G1000_loci_hg19.zip"
+ ascat_min_base_qual = 30
+ chr_dir = "${params.modules_testdata_base_path}/genomics/homo_sapiens/genome/chr21/sequence/chromosomes.tar.gz"
+ germline_resource = "${params.modules_testdata_base_path}/genomics/homo_sapiens/genome/chr21/germlineresources/gnomAD.r2.1.1.vcf.gz"
+ intervals = "${params.modules_testdata_base_path}/genomics/homo_sapiens/genome/chr21/sequence/multi_intervals.bed"
+ step = 'variant_calling'
+ tools = 'ascat'
+ wes = false
}
diff --git a/conf/test/tools_tumoronly.config b/conf/test/tools_tumoronly.config
index b113fa76fd..daf931d964 100644
--- a/conf/test/tools_tumoronly.config
+++ b/conf/test/tools_tumoronly.config
@@ -11,11 +11,18 @@
params {
input = "${projectDir}/tests/csv/3.0/recalibrated_tumoronly.csv"
- dbsnp = params.test_data['homo_sapiens']['genome']['dbsnp_138_hg38_21_vcf_gz']
- fasta = params.test_data['homo_sapiens']['genome']['genome_21_fasta']
- germline_resource = params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_21_vcf_gz']
- intervals = params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed']
- pon = params.test_data['homo_sapiens']['genome']['mills_and_1000g_indels_21_vcf_gz']
+ genome = null
+ igenomes_ignore = true
+ dbsnp = "${params.modules_testdata_base_path}/genomics/homo_sapiens/genome/chr21/germlineresources/dbsnp_138.hg38.vcf.gz"
+ dbsnp_tbi = "${params.modules_testdata_base_path}/genomics/homo_sapiens/genome/chr21/germlineresources/dbsnp_138.hg38.vcf.gz.tbi"
+ fasta = "${params.modules_testdata_base_path}/genomics/homo_sapiens/genome/chr21/sequence/genome.fasta"
+ fasta_fai = "${params.modules_testdata_base_path}/genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai"
+ germline_resource = "${params.modules_testdata_base_path}/genomics/homo_sapiens/genome/chr21/germlineresources/gnomAD.r2.1.1.vcf.gz"
+ germline_resource_tbi = "${params.modules_testdata_base_path}/genomics/homo_sapiens/genome/chr21/germlineresources/gnomAD.r2.1.1.vcf.gz.tbi"
+ intervals = "${params.modules_testdata_base_path}/genomics/homo_sapiens/genome/chr21/sequence/multi_intervals.bed"
+ pon = "${params.modules_testdata_base_path}/genomics/homo_sapiens/genome/chr21/germlineresources/mills_and_1000G.indels.hg38.vcf.gz"
+ pon_tbi = "${params.modules_testdata_base_path}/genomics/homo_sapiens/genome/chr21/germlineresources/mills_and_1000G.indels.hg38.vcf.gz.tbi"
+ ngscheckmate_bed = "${params.modules_testdata_base_path}/genomics/homo_sapiens/genome/chr21/germlineresources/SNP_GRCh38_hg38_wChr.bed"
nucleotides_per_second = 20
step = 'variant_calling'
tools = null
diff --git a/conf/test/use_gatk_spark.config b/conf/test/use_gatk_spark.config
index bd40af1b77..43443d7e2a 100644
--- a/conf/test/use_gatk_spark.config
+++ b/conf/test/use_gatk_spark.config
@@ -10,7 +10,7 @@
*/
params {
+ input = "${projectDir}/tests/csv/3.0/fastq_tumor_only.csv"
tools = null
use_gatk_spark = 'baserecalibrator,markduplicates'
- input = "${projectDir}/tests/csv/3.0/fastq_tumor_only.csv"
}
diff --git a/conf/test/variantcalling_channels.config b/conf/test/variantcalling_channels.config
index a6ff70387a..572a2e18ea 100644
--- a/conf/test/variantcalling_channels.config
+++ b/conf/test/variantcalling_channels.config
@@ -11,8 +11,12 @@
params {
input = "${projectDir}/tests/csv/3.0/recalibrated.csv"
- fasta = params.test_data['homo_sapiens']['genome']['genome_21_fasta']
- intervals = params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed']
+ genome = null
+ igenomes_ignore = true
+ fasta = "${params.modules_testdata_base_path}/genomics/homo_sapiens/genome/chr21/sequence/genome.fasta"
+ fasta_fai = "${params.modules_testdata_base_path}/genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai"
+ intervals = "${params.modules_testdata_base_path}/genomics/homo_sapiens/genome/chr21/sequence/multi_intervals.bed"
+ ngscheckmate_bed = "${params.modules_testdata_base_path}/genomics/homo_sapiens/genome/chr21/germlineresources/SNP_GRCh38_hg38_wChr.bed"
nucleotides_per_second = 20
step = 'variant_calling'
tools = null
diff --git a/main.nf b/main.nf
index 8b7940a558..9c272624fb 100755
--- a/main.nf
+++ b/main.nf
@@ -162,7 +162,7 @@ workflow NFCORE_SAREK {
: PREPARE_GENOME.out.hashtable
// Gather index for mapping given the chosen aligner
- index_alignement = (aligner == "bwa-mem" || aligner == "sentieon-bwamem") ? bwa :
+ index_alignment = (aligner == "bwa-mem" || aligner == "sentieon-bwamem") ? bwa :
aligner == "bwa-mem2" ? bwamem2 :
dragmap
@@ -177,12 +177,12 @@ workflow NFCORE_SAREK {
rt_file = PREPARE_GENOME.out.rt_file
// Tabix indexed vcf files
- bcftools_annotations_tbi = params.bcftools_annotations ? params.bcftools_annotations_tbi ? Channel.fromPath(params.bcftools_annotations_tbi) : PREPARE_GENOME.out.bcftools_annotations_tbi : Channel.empty([])
- dbsnp_tbi = params.dbsnp ? params.dbsnp_tbi ? Channel.fromPath(params.dbsnp_tbi) : PREPARE_GENOME.out.dbsnp_tbi : Channel.value([])
- germline_resource_tbi = params.germline_resource ? params.germline_resource_tbi ? Channel.fromPath(params.germline_resource_tbi) : PREPARE_GENOME.out.germline_resource_tbi : [] //do not change to Channel.value([]), the check for its existence then fails for Getpileupsumamries
- known_indels_tbi = params.known_indels ? params.known_indels_tbi ? Channel.fromPath(params.known_indels_tbi).collect() : PREPARE_GENOME.out.known_indels_tbi : Channel.value([])
- known_snps_tbi = params.known_snps ? params.known_snps_tbi ? Channel.fromPath(params.known_snps_tbi) : PREPARE_GENOME.out.known_snps_tbi : Channel.value([])
- pon_tbi = params.pon ? params.pon_tbi ? Channel.fromPath(params.pon_tbi) : PREPARE_GENOME.out.pon_tbi : Channel.value([])
+ bcftools_annotations_tbi = params.bcftools_annotations ? params.bcftools_annotations_tbi ? Channel.fromPath(params.bcftools_annotations_tbi).collect() : PREPARE_GENOME.out.bcftools_annotations_tbi : Channel.empty([])
+ dbsnp_tbi = params.dbsnp ? params.dbsnp_tbi ? Channel.fromPath(params.dbsnp_tbi).collect() : PREPARE_GENOME.out.dbsnp_tbi : Channel.value([])
+ germline_resource_tbi = params.germline_resource ? params.germline_resource_tbi ? Channel.fromPath(params.germline_resource_tbi).collect() : PREPARE_GENOME.out.germline_resource_tbi : [] //do not change to Channel.value([]), the check for its existence then fails for Getpileupsumamries
+ known_indels_tbi = params.known_indels ? params.known_indels_tbi ? Channel.fromPath(params.known_indels_tbi).collect() : PREPARE_GENOME.out.known_indels_tbi : Channel.value([])
+ known_snps_tbi = params.known_snps ? params.known_snps_tbi ? Channel.fromPath(params.known_snps_tbi).collect() : PREPARE_GENOME.out.known_snps_tbi : Channel.value([])
+ pon_tbi = params.pon ? params.pon_tbi ? Channel.fromPath(params.pon_tbi).collect() : PREPARE_GENOME.out.pon_tbi : Channel.value([])
// known_sites is made by grouping both the dbsnp and the known snps/indels resources
// Which can either or both be optional
@@ -279,7 +279,7 @@ workflow NFCORE_SAREK {
gc_file,
germline_resource,
germline_resource_tbi,
- index_alignement,
+ index_alignment,
intervals_and_num_intervals,
intervals_bed_combined,
intervals_bed_combined_for_variant_calling,
diff --git a/modules.json b/modules.json
index a3f3a8fd65..a64bdb2c7d 100644
--- a/modules.json
+++ b/modules.json
@@ -316,7 +316,7 @@
},
"mosdepth": {
"branch": "master",
- "git_sha": "30d3ca4346ae38f0de821c57a9c517b8b0b135d6",
+ "git_sha": "e0616fba0919adb190bfe070d17fb12d76ba3a26",
"installed_by": ["modules"]
},
"msisensorpro/msisomatic": {
@@ -391,42 +391,42 @@
},
"sentieon/applyvarcal": {
"branch": "master",
- "git_sha": "220da1aa7d6ab6555817035041dd2fc05cb518d3",
+ "git_sha": "e809c6b078d5343bdf8b5b2b78483096a2b5a973",
"installed_by": ["modules"]
},
"sentieon/bwamem": {
"branch": "master",
- "git_sha": "220da1aa7d6ab6555817035041dd2fc05cb518d3",
+ "git_sha": "e809c6b078d5343bdf8b5b2b78483096a2b5a973",
"installed_by": ["modules"]
},
"sentieon/dedup": {
"branch": "master",
- "git_sha": "220da1aa7d6ab6555817035041dd2fc05cb518d3",
+ "git_sha": "e809c6b078d5343bdf8b5b2b78483096a2b5a973",
"installed_by": ["modules"]
},
"sentieon/dnamodelapply": {
"branch": "master",
- "git_sha": "220da1aa7d6ab6555817035041dd2fc05cb518d3",
+ "git_sha": "e809c6b078d5343bdf8b5b2b78483096a2b5a973",
"installed_by": ["modules"]
},
"sentieon/dnascope": {
"branch": "master",
- "git_sha": "220da1aa7d6ab6555817035041dd2fc05cb518d3",
+ "git_sha": "e809c6b078d5343bdf8b5b2b78483096a2b5a973",
"installed_by": ["modules"]
},
"sentieon/gvcftyper": {
"branch": "master",
- "git_sha": "220da1aa7d6ab6555817035041dd2fc05cb518d3",
+ "git_sha": "e809c6b078d5343bdf8b5b2b78483096a2b5a973",
"installed_by": ["modules"]
},
"sentieon/haplotyper": {
"branch": "master",
- "git_sha": "220da1aa7d6ab6555817035041dd2fc05cb518d3",
+ "git_sha": "e809c6b078d5343bdf8b5b2b78483096a2b5a973",
"installed_by": ["modules"]
},
"sentieon/varcal": {
"branch": "master",
- "git_sha": "220da1aa7d6ab6555817035041dd2fc05cb518d3",
+ "git_sha": "e809c6b078d5343bdf8b5b2b78483096a2b5a973",
"installed_by": ["modules"]
},
"snpeff/download": {
@@ -500,7 +500,7 @@
},
"utils_nfcore_pipeline": {
"branch": "master",
- "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa",
+ "git_sha": "92de218a329bfc9a9033116eb5f65fd270e72ba3",
"installed_by": ["subworkflows"]
},
"utils_nfvalidation_plugin": {
diff --git a/modules/nf-core/mosdepth/environment.yml b/modules/nf-core/mosdepth/environment.yml
index 88c7126c05..bcb9d64a7a 100644
--- a/modules/nf-core/mosdepth/environment.yml
+++ b/modules/nf-core/mosdepth/environment.yml
@@ -5,4 +5,4 @@ channels:
- defaults
dependencies:
# renovate: datasource=conda depName=bioconda/mosdepth
- - mosdepth=0.3.6
+ - mosdepth=0.3.8
diff --git a/modules/nf-core/mosdepth/main.nf b/modules/nf-core/mosdepth/main.nf
index 0190a09d80..6f4a838343 100644
--- a/modules/nf-core/mosdepth/main.nf
+++ b/modules/nf-core/mosdepth/main.nf
@@ -4,8 +4,8 @@ process MOSDEPTH {
conda "${moduleDir}/environment.yml"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
- 'https://depot.galaxyproject.org/singularity/mosdepth:0.3.6--hd299d5a_0' :
- 'biocontainers/mosdepth:0.3.6--hd299d5a_0'}"
+ 'https://depot.galaxyproject.org/singularity/mosdepth:0.3.8--hd299d5a_0' :
+ 'biocontainers/mosdepth:0.3.8--hd299d5a_0'}"
input:
tuple val(meta), path(bam), path(bai), path(bed)
diff --git a/modules/nf-core/mosdepth/tests/main.nf.test.snap b/modules/nf-core/mosdepth/tests/main.nf.test.snap
index 00f4cd974b..c604540b03 100644
--- a/modules/nf-core/mosdepth/tests/main.nf.test.snap
+++ b/modules/nf-core/mosdepth/tests/main.nf.test.snap
@@ -39,7 +39,7 @@
]
],
"12": [
- "versions.yml:md5,f8b1896c9c6784181f1234e87225f0e8"
+ "versions.yml:md5,87634e525fb18990cd98fe1080ad72ce"
],
"2": [
[
@@ -222,15 +222,15 @@
]
],
"versions": [
- "versions.yml:md5,f8b1896c9c6784181f1234e87225f0e8"
+ "versions.yml:md5,87634e525fb18990cd98fe1080ad72ce"
]
}
],
"meta": {
"nf-test": "0.8.4",
- "nextflow": "23.10.0"
+ "nextflow": "23.10.1"
},
- "timestamp": "2024-03-28T12:29:04.084192"
+ "timestamp": "2024-04-29T13:33:16.953408231"
},
"homo_sapiens - cram, crai, bed": {
"content": [
@@ -260,7 +260,7 @@
],
"12": [
- "versions.yml:md5,f8b1896c9c6784181f1234e87225f0e8"
+ "versions.yml:md5,87634e525fb18990cd98fe1080ad72ce"
],
"2": [
[
@@ -289,7 +289,7 @@
"id": "test",
"single_end": true
},
- "test.per-base.bed.gz.csi:md5,9e649ac749ff6c6073bef5ab63e8aaa4"
+ "test.per-base.bed.gz.csi:md5,6f322dc9250522a701bd68bd18fa8294"
]
],
"6": [
@@ -307,7 +307,7 @@
"id": "test",
"single_end": true
},
- "test.regions.bed.gz.csi:md5,47669cfe41f3e222e74d81e1b1be191f"
+ "test.regions.bed.gz.csi:md5,e7df086f0a36e88ca231e143d43bd3f9"
]
],
"8": [
@@ -340,7 +340,7 @@
"id": "test",
"single_end": true
},
- "test.per-base.bed.gz.csi:md5,9e649ac749ff6c6073bef5ab63e8aaa4"
+ "test.per-base.bed.gz.csi:md5,6f322dc9250522a701bd68bd18fa8294"
]
],
"per_base_d4": [
@@ -367,7 +367,7 @@
"id": "test",
"single_end": true
},
- "test.regions.bed.gz.csi:md5,47669cfe41f3e222e74d81e1b1be191f"
+ "test.regions.bed.gz.csi:md5,e7df086f0a36e88ca231e143d43bd3f9"
]
],
"regions_txt": [
@@ -395,15 +395,15 @@
],
"versions": [
- "versions.yml:md5,f8b1896c9c6784181f1234e87225f0e8"
+ "versions.yml:md5,87634e525fb18990cd98fe1080ad72ce"
]
}
],
"meta": {
"nf-test": "0.8.4",
- "nextflow": "23.10.0"
+ "nextflow": "23.10.1"
},
- "timestamp": "2024-03-28T12:28:16.664319"
+ "timestamp": "2024-04-29T13:32:50.160217828"
},
"homo_sapiens - bam, bai, [] - quantized": {
"content": [
@@ -433,7 +433,7 @@
],
"12": [
- "versions.yml:md5,f8b1896c9c6784181f1234e87225f0e8"
+ "versions.yml:md5,87634e525fb18990cd98fe1080ad72ce"
],
"2": [
@@ -456,7 +456,7 @@
"id": "test",
"single_end": true
},
- "test.per-base.bed.gz.csi:md5,9e649ac749ff6c6073bef5ab63e8aaa4"
+ "test.per-base.bed.gz.csi:md5,6f322dc9250522a701bd68bd18fa8294"
]
],
"6": [
@@ -480,7 +480,7 @@
"id": "test",
"single_end": true
},
- "test.quantized.bed.gz.csi:md5,be9617f551f19a33923f1e886eaefb93"
+ "test.quantized.bed.gz.csi:md5,4f69e6ace50206a2768be66ded3a56f0"
]
],
"global_txt": [
@@ -507,7 +507,7 @@
"id": "test",
"single_end": true
},
- "test.per-base.bed.gz.csi:md5,9e649ac749ff6c6073bef5ab63e8aaa4"
+ "test.per-base.bed.gz.csi:md5,6f322dc9250522a701bd68bd18fa8294"
]
],
"per_base_d4": [
@@ -528,7 +528,7 @@
"id": "test",
"single_end": true
},
- "test.quantized.bed.gz.csi:md5,be9617f551f19a33923f1e886eaefb93"
+ "test.quantized.bed.gz.csi:md5,4f69e6ace50206a2768be66ded3a56f0"
]
],
"regions_bed": [
@@ -556,15 +556,15 @@
],
"versions": [
- "versions.yml:md5,f8b1896c9c6784181f1234e87225f0e8"
+ "versions.yml:md5,87634e525fb18990cd98fe1080ad72ce"
]
}
],
"meta": {
"nf-test": "0.8.4",
- "nextflow": "23.10.0"
+ "nextflow": "23.10.1"
},
- "timestamp": "2024-03-28T12:28:35.978752"
+ "timestamp": "2024-04-29T13:33:01.164885111"
},
"homo_sapiens - bam, bai, bed": {
"content": [
@@ -594,7 +594,7 @@
],
"12": [
- "versions.yml:md5,f8b1896c9c6784181f1234e87225f0e8"
+ "versions.yml:md5,87634e525fb18990cd98fe1080ad72ce"
],
"2": [
[
@@ -623,7 +623,7 @@
"id": "test",
"single_end": true
},
- "test.per-base.bed.gz.csi:md5,9e649ac749ff6c6073bef5ab63e8aaa4"
+ "test.per-base.bed.gz.csi:md5,6f322dc9250522a701bd68bd18fa8294"
]
],
"6": [
@@ -641,7 +641,7 @@
"id": "test",
"single_end": true
},
- "test.regions.bed.gz.csi:md5,47669cfe41f3e222e74d81e1b1be191f"
+ "test.regions.bed.gz.csi:md5,e7df086f0a36e88ca231e143d43bd3f9"
]
],
"8": [
@@ -674,7 +674,7 @@
"id": "test",
"single_end": true
},
- "test.per-base.bed.gz.csi:md5,9e649ac749ff6c6073bef5ab63e8aaa4"
+ "test.per-base.bed.gz.csi:md5,6f322dc9250522a701bd68bd18fa8294"
]
],
"per_base_d4": [
@@ -701,7 +701,7 @@
"id": "test",
"single_end": true
},
- "test.regions.bed.gz.csi:md5,47669cfe41f3e222e74d81e1b1be191f"
+ "test.regions.bed.gz.csi:md5,e7df086f0a36e88ca231e143d43bd3f9"
]
],
"regions_txt": [
@@ -729,15 +729,15 @@
],
"versions": [
- "versions.yml:md5,f8b1896c9c6784181f1234e87225f0e8"
+ "versions.yml:md5,87634e525fb18990cd98fe1080ad72ce"
]
}
],
"meta": {
"nf-test": "0.8.4",
- "nextflow": "23.10.0"
+ "nextflow": "23.10.1"
},
- "timestamp": "2024-03-28T12:27:55.598384"
+ "timestamp": "2024-04-29T13:32:39.071657456"
},
"homo_sapiens - bam, bai, [] - window": {
"content": [
@@ -767,7 +767,7 @@
],
"12": [
- "versions.yml:md5,f8b1896c9c6784181f1234e87225f0e8"
+ "versions.yml:md5,87634e525fb18990cd98fe1080ad72ce"
],
"2": [
[
@@ -775,7 +775,7 @@
"id": "test",
"single_end": true
},
- "test.mosdepth.region.dist.txt:md5,39e0e707ec32feb5176fd20a95f1f468"
+ "test.mosdepth.region.dist.txt:md5,0b6ea9f0da1228252d9aef2d3b6f7f76"
]
],
"3": [
@@ -796,7 +796,7 @@
"id": "test",
"single_end": true
},
- "test.per-base.bed.gz.csi:md5,9e649ac749ff6c6073bef5ab63e8aaa4"
+ "test.per-base.bed.gz.csi:md5,6f322dc9250522a701bd68bd18fa8294"
]
],
"6": [
@@ -814,7 +814,7 @@
"id": "test",
"single_end": true
},
- "test.regions.bed.gz.csi:md5,257d67678136963d9dd904330079609d"
+ "test.regions.bed.gz.csi:md5,2a30bcb7f5c7632136b3efce24723970"
]
],
"8": [
@@ -847,7 +847,7 @@
"id": "test",
"single_end": true
},
- "test.per-base.bed.gz.csi:md5,9e649ac749ff6c6073bef5ab63e8aaa4"
+ "test.per-base.bed.gz.csi:md5,6f322dc9250522a701bd68bd18fa8294"
]
],
"per_base_d4": [
@@ -874,7 +874,7 @@
"id": "test",
"single_end": true
},
- "test.regions.bed.gz.csi:md5,257d67678136963d9dd904330079609d"
+ "test.regions.bed.gz.csi:md5,2a30bcb7f5c7632136b3efce24723970"
]
],
"regions_txt": [
@@ -883,7 +883,7 @@
"id": "test",
"single_end": true
},
- "test.mosdepth.region.dist.txt:md5,39e0e707ec32feb5176fd20a95f1f468"
+ "test.mosdepth.region.dist.txt:md5,0b6ea9f0da1228252d9aef2d3b6f7f76"
]
],
"summary_txt": [
@@ -902,15 +902,15 @@
],
"versions": [
- "versions.yml:md5,f8b1896c9c6784181f1234e87225f0e8"
+ "versions.yml:md5,87634e525fb18990cd98fe1080ad72ce"
]
}
],
"meta": {
"nf-test": "0.8.4",
- "nextflow": "23.10.0"
+ "nextflow": "23.10.1"
},
- "timestamp": "2024-03-28T12:28:26.37386"
+ "timestamp": "2024-04-29T13:32:55.631776118"
},
"homo_sapiens - bam, bai, []": {
"content": [
@@ -940,7 +940,7 @@
],
"12": [
- "versions.yml:md5,f8b1896c9c6784181f1234e87225f0e8"
+ "versions.yml:md5,87634e525fb18990cd98fe1080ad72ce"
],
"2": [
@@ -963,7 +963,7 @@
"id": "test",
"single_end": true
},
- "test.per-base.bed.gz.csi:md5,9e649ac749ff6c6073bef5ab63e8aaa4"
+ "test.per-base.bed.gz.csi:md5,6f322dc9250522a701bd68bd18fa8294"
]
],
"6": [
@@ -1002,7 +1002,7 @@
"id": "test",
"single_end": true
},
- "test.per-base.bed.gz.csi:md5,9e649ac749ff6c6073bef5ab63e8aaa4"
+ "test.per-base.bed.gz.csi:md5,6f322dc9250522a701bd68bd18fa8294"
]
],
"per_base_d4": [
@@ -1039,15 +1039,15 @@
],
"versions": [
- "versions.yml:md5,f8b1896c9c6784181f1234e87225f0e8"
+ "versions.yml:md5,87634e525fb18990cd98fe1080ad72ce"
]
}
],
"meta": {
"nf-test": "0.8.4",
- "nextflow": "23.10.0"
+ "nextflow": "23.10.1"
},
- "timestamp": "2024-03-28T12:27:44.658599"
+ "timestamp": "2024-04-29T13:32:33.642125299"
},
"homo_sapiens - cram, crai, []": {
"content": [
@@ -1077,7 +1077,7 @@
],
"12": [
- "versions.yml:md5,f8b1896c9c6784181f1234e87225f0e8"
+ "versions.yml:md5,87634e525fb18990cd98fe1080ad72ce"
],
"2": [
@@ -1100,7 +1100,7 @@
"id": "test",
"single_end": true
},
- "test.per-base.bed.gz.csi:md5,9e649ac749ff6c6073bef5ab63e8aaa4"
+ "test.per-base.bed.gz.csi:md5,6f322dc9250522a701bd68bd18fa8294"
]
],
"6": [
@@ -1139,7 +1139,7 @@
"id": "test",
"single_end": true
},
- "test.per-base.bed.gz.csi:md5,9e649ac749ff6c6073bef5ab63e8aaa4"
+ "test.per-base.bed.gz.csi:md5,6f322dc9250522a701bd68bd18fa8294"
]
],
"per_base_d4": [
@@ -1176,15 +1176,15 @@
],
"versions": [
- "versions.yml:md5,f8b1896c9c6784181f1234e87225f0e8"
+ "versions.yml:md5,87634e525fb18990cd98fe1080ad72ce"
]
}
],
"meta": {
"nf-test": "0.8.4",
- "nextflow": "23.10.0"
+ "nextflow": "23.10.1"
},
- "timestamp": "2024-03-28T12:28:06.482838"
+ "timestamp": "2024-04-29T13:32:44.704920941"
},
"homo_sapiens - bam, bai, bed - thresholds": {
"content": [
@@ -1222,11 +1222,11 @@
"id": "test",
"single_end": true
},
- "test.thresholds.bed.gz.csi:md5,912055ee9452229439df6fae95644196"
+ "test.thresholds.bed.gz.csi:md5,219414a0751185adb98d2235d83ea055"
]
],
"12": [
- "versions.yml:md5,f8b1896c9c6784181f1234e87225f0e8"
+ "versions.yml:md5,87634e525fb18990cd98fe1080ad72ce"
],
"2": [
[
@@ -1255,7 +1255,7 @@
"id": "test",
"single_end": true
},
- "test.per-base.bed.gz.csi:md5,9e649ac749ff6c6073bef5ab63e8aaa4"
+ "test.per-base.bed.gz.csi:md5,6f322dc9250522a701bd68bd18fa8294"
]
],
"6": [
@@ -1273,7 +1273,7 @@
"id": "test",
"single_end": true
},
- "test.regions.bed.gz.csi:md5,47669cfe41f3e222e74d81e1b1be191f"
+ "test.regions.bed.gz.csi:md5,e7df086f0a36e88ca231e143d43bd3f9"
]
],
"8": [
@@ -1306,7 +1306,7 @@
"id": "test",
"single_end": true
},
- "test.per-base.bed.gz.csi:md5,9e649ac749ff6c6073bef5ab63e8aaa4"
+ "test.per-base.bed.gz.csi:md5,6f322dc9250522a701bd68bd18fa8294"
]
],
"per_base_d4": [
@@ -1333,7 +1333,7 @@
"id": "test",
"single_end": true
},
- "test.regions.bed.gz.csi:md5,47669cfe41f3e222e74d81e1b1be191f"
+ "test.regions.bed.gz.csi:md5,e7df086f0a36e88ca231e143d43bd3f9"
]
],
"regions_txt": [
@@ -1369,18 +1369,18 @@
"id": "test",
"single_end": true
},
- "test.thresholds.bed.gz.csi:md5,912055ee9452229439df6fae95644196"
+ "test.thresholds.bed.gz.csi:md5,219414a0751185adb98d2235d83ea055"
]
],
"versions": [
- "versions.yml:md5,f8b1896c9c6784181f1234e87225f0e8"
+ "versions.yml:md5,87634e525fb18990cd98fe1080ad72ce"
]
}
],
"meta": {
"nf-test": "0.8.4",
- "nextflow": "23.10.0"
+ "nextflow": "23.10.1"
},
- "timestamp": "2024-03-28T12:28:45.918241"
+ "timestamp": "2024-04-29T13:33:06.737266831"
}
}
\ No newline at end of file
diff --git a/modules/nf-core/sentieon/applyvarcal/environment.yml b/modules/nf-core/sentieon/applyvarcal/environment.yml
index c4c11b1f85..0af79bedcd 100644
--- a/modules/nf-core/sentieon/applyvarcal/environment.yml
+++ b/modules/nf-core/sentieon/applyvarcal/environment.yml
@@ -4,4 +4,4 @@ channels:
- bioconda
- defaults
dependencies:
- - bioconda::sentieon=202308.01
+ - bioconda::sentieon=202308.02
diff --git a/modules/nf-core/sentieon/applyvarcal/main.nf b/modules/nf-core/sentieon/applyvarcal/main.nf
index d1d3435dc9..6e5e863c51 100644
--- a/modules/nf-core/sentieon/applyvarcal/main.nf
+++ b/modules/nf-core/sentieon/applyvarcal/main.nf
@@ -7,8 +7,8 @@ process SENTIEON_APPLYVARCAL {
conda "${moduleDir}/environment.yml"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
- 'https://depot.galaxyproject.org/singularity/sentieon:202308.01--h43eeafb_0' :
- 'biocontainers/sentieon:202308.01--h43eeafb_0' }"
+ 'https://depot.galaxyproject.org/singularity/sentieon:202308.02--h43eeafb_0' :
+ 'biocontainers/sentieon:202308.02--h43eeafb_0' }"
input:
tuple val(meta), path(vcf), path(vcf_tbi), path(recal), path(recal_index), path(tranches)
diff --git a/modules/nf-core/sentieon/bwamem/environment.yml b/modules/nf-core/sentieon/bwamem/environment.yml
index c090bfa5ae..f03db6f8a3 100644
--- a/modules/nf-core/sentieon/bwamem/environment.yml
+++ b/modules/nf-core/sentieon/bwamem/environment.yml
@@ -4,4 +4,4 @@ channels:
- bioconda
- defaults
dependencies:
- - bioconda::sentieon=202308.01
+ - bioconda::sentieon=202308.02
diff --git a/modules/nf-core/sentieon/bwamem/main.nf b/modules/nf-core/sentieon/bwamem/main.nf
index 230297d087..62693851c3 100644
--- a/modules/nf-core/sentieon/bwamem/main.nf
+++ b/modules/nf-core/sentieon/bwamem/main.nf
@@ -7,8 +7,8 @@ process SENTIEON_BWAMEM {
conda "${moduleDir}/environment.yml"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
- 'https://depot.galaxyproject.org/singularity/sentieon:202308.01--h43eeafb_0' :
- 'biocontainers/sentieon:202308.01--h43eeafb_0' }"
+ 'https://depot.galaxyproject.org/singularity/sentieon:202308.02--h43eeafb_0' :
+ 'biocontainers/sentieon:202308.02--h43eeafb_0' }"
input:
tuple val(meta), path(reads)
diff --git a/modules/nf-core/sentieon/dedup/environment.yml b/modules/nf-core/sentieon/dedup/environment.yml
index 622cf73909..e29cfff3e4 100644
--- a/modules/nf-core/sentieon/dedup/environment.yml
+++ b/modules/nf-core/sentieon/dedup/environment.yml
@@ -4,4 +4,4 @@ channels:
- bioconda
- defaults
dependencies:
- - bioconda::sentieon=202308.01
+ - bioconda::sentieon=202308.02
diff --git a/modules/nf-core/sentieon/dedup/main.nf b/modules/nf-core/sentieon/dedup/main.nf
index fbcd595f47..5f19ab56d8 100644
--- a/modules/nf-core/sentieon/dedup/main.nf
+++ b/modules/nf-core/sentieon/dedup/main.nf
@@ -7,8 +7,8 @@ process SENTIEON_DEDUP {
conda "${moduleDir}/environment.yml"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
- 'https://depot.galaxyproject.org/singularity/sentieon:202308.01--h43eeafb_0' :
- 'biocontainers/sentieon:202308.01--h43eeafb_0' }"
+ 'https://depot.galaxyproject.org/singularity/sentieon:202308.02--h43eeafb_0' :
+ 'biocontainers/sentieon:202308.02--h43eeafb_0' }"
input:
tuple val(meta), path(bam), path(bai)
diff --git a/modules/nf-core/sentieon/dnamodelapply/environment.yml b/modules/nf-core/sentieon/dnamodelapply/environment.yml
index 6d27d44a1d..a2f8819313 100644
--- a/modules/nf-core/sentieon/dnamodelapply/environment.yml
+++ b/modules/nf-core/sentieon/dnamodelapply/environment.yml
@@ -4,4 +4,4 @@ channels:
- bioconda
- defaults
dependencies:
- - bioconda::sentieon=202308.01
+ - bioconda::sentieon=202308.02
diff --git a/modules/nf-core/sentieon/dnamodelapply/main.nf b/modules/nf-core/sentieon/dnamodelapply/main.nf
index b728a5ec31..9a0c70dc22 100644
--- a/modules/nf-core/sentieon/dnamodelapply/main.nf
+++ b/modules/nf-core/sentieon/dnamodelapply/main.nf
@@ -7,8 +7,8 @@ process SENTIEON_DNAMODELAPPLY {
conda "${moduleDir}/environment.yml"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
- 'https://depot.galaxyproject.org/singularity/sentieon:202308.01--h43eeafb_0' :
- 'biocontainers/sentieon:202308.01--h43eeafb_0' }"
+ 'https://depot.galaxyproject.org/singularity/sentieon:202308.02--h43eeafb_0' :
+ 'biocontainers/sentieon:202308.02--h43eeafb_0' }"
input:
tuple val(meta), path(vcf), path(idx)
diff --git a/modules/nf-core/sentieon/dnascope/environment.yml b/modules/nf-core/sentieon/dnascope/environment.yml
index 45c2116c04..e6da2dde3e 100644
--- a/modules/nf-core/sentieon/dnascope/environment.yml
+++ b/modules/nf-core/sentieon/dnascope/environment.yml
@@ -4,4 +4,4 @@ channels:
- bioconda
- defaults
dependencies:
- - bioconda::sentieon=202308.01
+ - bioconda::sentieon=202308.02
diff --git a/modules/nf-core/sentieon/dnascope/main.nf b/modules/nf-core/sentieon/dnascope/main.nf
index 6adea35eea..0671307ba0 100644
--- a/modules/nf-core/sentieon/dnascope/main.nf
+++ b/modules/nf-core/sentieon/dnascope/main.nf
@@ -7,8 +7,8 @@ process SENTIEON_DNASCOPE {
conda "${moduleDir}/environment.yml"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
- 'https://depot.galaxyproject.org/singularity/sentieon:202308.01--h43eeafb_0' :
- 'biocontainers/sentieon:202308.01--h43eeafb_0' }"
+ 'https://depot.galaxyproject.org/singularity/sentieon:202308.02--h43eeafb_0' :
+ 'biocontainers/sentieon:202308.02--h43eeafb_0' }"
input:
tuple val(meta), path(bam), path(bai), path(intervals)
diff --git a/modules/nf-core/sentieon/gvcftyper/environment.yml b/modules/nf-core/sentieon/gvcftyper/environment.yml
index 9a8143068a..732e2ca846 100644
--- a/modules/nf-core/sentieon/gvcftyper/environment.yml
+++ b/modules/nf-core/sentieon/gvcftyper/environment.yml
@@ -4,4 +4,4 @@ channels:
- bioconda
- defaults
dependencies:
- - bioconda::sentieon=202308.01
+ - bioconda::sentieon=202308.02
diff --git a/modules/nf-core/sentieon/gvcftyper/main.nf b/modules/nf-core/sentieon/gvcftyper/main.nf
index 4b5c9df4e3..7539214507 100644
--- a/modules/nf-core/sentieon/gvcftyper/main.nf
+++ b/modules/nf-core/sentieon/gvcftyper/main.nf
@@ -7,8 +7,8 @@ process SENTIEON_GVCFTYPER {
conda "${moduleDir}/environment.yml"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
- 'https://depot.galaxyproject.org/singularity/sentieon:202308.01--h43eeafb_0' :
- 'biocontainers/sentieon:202308.01--h43eeafb_0' }"
+ 'https://depot.galaxyproject.org/singularity/sentieon:202308.02--h43eeafb_0' :
+ 'biocontainers/sentieon:202308.02--h43eeafb_0' }"
input:
tuple val(meta), path(gvcfs), path(tbis), path(intervals)
diff --git a/modules/nf-core/sentieon/haplotyper/environment.yml b/modules/nf-core/sentieon/haplotyper/environment.yml
index a3a721cf1d..89108f8e8b 100644
--- a/modules/nf-core/sentieon/haplotyper/environment.yml
+++ b/modules/nf-core/sentieon/haplotyper/environment.yml
@@ -4,4 +4,4 @@ channels:
- bioconda
- defaults
dependencies:
- - bioconda::sentieon=202308.01
+ - bioconda::sentieon=202308.02
diff --git a/modules/nf-core/sentieon/haplotyper/main.nf b/modules/nf-core/sentieon/haplotyper/main.nf
index 87a9343474..16eb775744 100644
--- a/modules/nf-core/sentieon/haplotyper/main.nf
+++ b/modules/nf-core/sentieon/haplotyper/main.nf
@@ -7,8 +7,8 @@ process SENTIEON_HAPLOTYPER {
conda "${moduleDir}/environment.yml"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
- 'https://depot.galaxyproject.org/singularity/sentieon:202308.01--h43eeafb_0' :
- 'biocontainers/sentieon:202308.01--h43eeafb_0' }"
+ 'https://depot.galaxyproject.org/singularity/sentieon:202308.02--h43eeafb_0' :
+ 'biocontainers/sentieon:202308.02--h43eeafb_0' }"
input:
tuple val(meta), path(input), path(input_index), path(intervals)
diff --git a/modules/nf-core/sentieon/varcal/environment.yml b/modules/nf-core/sentieon/varcal/environment.yml
index 93921ff046..481da2ce84 100644
--- a/modules/nf-core/sentieon/varcal/environment.yml
+++ b/modules/nf-core/sentieon/varcal/environment.yml
@@ -4,4 +4,4 @@ channels:
- bioconda
- defaults
dependencies:
- - bioconda::sentieon=202308.01
+ - bioconda::sentieon=202308.02
diff --git a/modules/nf-core/sentieon/varcal/main.nf b/modules/nf-core/sentieon/varcal/main.nf
index 17a3b71845..aa8847f839 100644
--- a/modules/nf-core/sentieon/varcal/main.nf
+++ b/modules/nf-core/sentieon/varcal/main.nf
@@ -7,8 +7,8 @@ process SENTIEON_VARCAL {
conda "${moduleDir}/environment.yml"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
- 'https://depot.galaxyproject.org/singularity/sentieon:202308.01--h43eeafb_0' :
- 'biocontainers/sentieon:202308.01--h43eeafb_0' }"
+ 'https://depot.galaxyproject.org/singularity/sentieon:202308.02--h43eeafb_0' :
+ 'biocontainers/sentieon:202308.02--h43eeafb_0' }"
input:
tuple val(meta), path(vcf), path(tbi) // input vcf and tbi of variants to recalibrate
diff --git a/nextflow.config b/nextflow.config
index a5526b67ce..f26930b9d1 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -247,6 +247,13 @@ profiles {
shifter.enabled = false
singularity.enabled = false
}
+ wave {
+ apptainer.ociAutoPull = true
+ singularity.ociAutoPull = true
+ wave.enabled = true
+ wave.freeze = true
+ wave.strategy = 'conda,container'
+ }
gitpod {
executor.cpus = 4
executor.memory = 8.GB
@@ -262,7 +269,6 @@ profiles {
includeConfig 'conf/test.config'
params.sentieon_dnascope_model = "az://igenomes/Homo_sapiens/GATK/GRCh38/Annotation/Sentieon/SentieonDNAscopeModel1.1.model"
}
- test_cache { includeConfig 'conf/test/cache.config' }
// Extra test profiles for full tests on AWS
test_full { includeConfig 'conf/test_full.config' }
test_full_aws {
@@ -330,7 +336,7 @@ singularity.registry = 'quay.io'
// Nextflow plugins
plugins {
id 'nf-validation@1.1.3' // Validation of pipeline parameters and creation of an input channel from a sample sheet
- id 'nf-prov' // Provenance reports for pipeline runs
+ id 'nf-prov@1.2.2' // Provenance reports for pipeline runs
}
// Load igenomes.config if required
@@ -390,8 +396,8 @@ manifest {
description = """An open-source analysis pipeline to detect germline or somatic variants from whole genome or targeted sequencing"""
mainScript = 'main.nf'
nextflowVersion = '!>=23.04.0'
- version = '3.4.1'
- doi = '10.12688/f1000research.16665.2, 10.1101/2023.07.19.549462, 10.5281/zenodo.3476425'
+ version = '3.4.2'
+ doi = '10.12688/f1000research.16665.2, 10.1093/nargab/lqae031, 10.5281/zenodo.3476425'
}
// Load modules.config for DSL2 module specific options
diff --git a/nextflow_schema.json b/nextflow_schema.json
index 0c58c57655..7545b9930e 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -576,7 +576,7 @@
"fa_icon": "fa-solid fa-text",
"description": "ASCAT genome.",
"help_text": "If you use AWS iGenomes, this has already been set for you appropriately.\n\nMust be set to run ASCAT, either hg19 or hg38. If you use AWS iGenomes, this has already been set for you appropriately.",
- "enum": ["None", "hg19", "hg38"],
+ "enum": ["hg19", "hg38"],
"hidden": true
},
"ascat_alleles": {
diff --git a/subworkflows/local/utils_nfcore_sarek_pipeline/main.nf b/subworkflows/local/utils_nfcore_sarek_pipeline/main.nf
index afd58a8cc2..0bd3c1364d 100644
--- a/subworkflows/local/utils_nfcore_sarek_pipeline/main.nf
+++ b/subworkflows/local/utils_nfcore_sarek_pipeline/main.nf
@@ -280,8 +280,16 @@ def methodsDescriptionText(mqc_methods_yaml) {
meta["manifest_map"] = workflow.manifest.toMap()
// Pipeline DOI
- meta["doi_text"] = meta.manifest_map.doi ? "(doi: ${meta.manifest_map.doi})" : ""
- meta["nodoi_text"] = meta.manifest_map.doi ? "": "If available, make sure to update the text to include the Zenodo DOI of version of the pipeline used. "
+ if (meta.manifest_map.doi) {
+ // Using a loop to handle multiple DOIs
+ // Removing `https://doi.org/` to handle pipelines using DOIs vs DOI resolvers
+ // Removing ` ` since the manifest.doi is a string and not a proper list
+ def temp_doi_ref = ""
+ String[] manifest_doi = meta.manifest_map.doi.tokenize(",")
+ for (String doi_ref: manifest_doi) temp_doi_ref += "(doi: ${doi_ref.replace("https://doi.org/", "").replace(" ", "")}), "
+ meta["doi_text"] = temp_doi_ref.substring(0, temp_doi_ref.length() - 2)
+ } else meta["doi_text"] = ""
+ meta["nodoi_text"] = meta.manifest_map.doi ? "" : "If available, make sure to update the text to include the Zenodo DOI of the pipeline version used. "
// Tool references
meta["tool_citations"] = ""
diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf
index a8b55d6fe1..14558c3927 100644
--- a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf
+++ b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf
@@ -65,9 +65,15 @@ def checkProfileProvided(nextflow_cli_args) {
// Citation string for pipeline
//
def workflowCitation() {
+ def temp_doi_ref = ""
+ String[] manifest_doi = workflow.manifest.doi.tokenize(",")
+ // Using a loop to handle multiple DOIs
+ // Removing `https://doi.org/` to handle pipelines using DOIs vs DOI resolvers
+ // Removing ` ` since the manifest.doi is a string and not a proper list
+ for (String doi_ref: manifest_doi) temp_doi_ref += " https://doi.org/${doi_ref.replace('https://doi.org/', '').replace(' ', '')}\n"
return "If you use ${workflow.manifest.name} for your analysis please cite:\n\n" +
"* The pipeline\n" +
- " ${workflow.manifest.doi}\n\n" +
+ temp_doi_ref + "\n" +
"* The nf-core framework\n" +
" https://doi.org/10.1038/s41587-020-0439-x\n\n" +
"* Software dependencies\n" +
diff --git a/tests/config/pytesttags.yml b/tests/config/pytesttags.yml
index 0c3c05c554..ac74cb8931 100644
--- a/tests/config/pytesttags.yml
+++ b/tests/config/pytesttags.yml
@@ -76,6 +76,7 @@ validation_checks:
alignment_to_fastq:
- conf/modules/alignment_to_fastq.config
- modules/nf-core/cat/fastq/**
+ - modules/nf-core/mosdepth/**
- modules/nf-core/samtools/collatefastq/**
- modules/nf-core/samtools/merge/**
- modules/nf-core/samtools/view/**
@@ -92,6 +93,7 @@ umi:
- modules/nf-core/fgbio/callmolecularconsensusreads/**
- modules/nf-core/fgbio/fastqtobam/**
- modules/nf-core/fgbio/groupreadsbyumi/**
+ - modules/nf-core/mosdepth/**
- modules/nf-core/samblaster/**
- modules/nf-core/samtools/bam2fq/**
- subworkflows/local/fastq_align_bwamem_mem2_dragmap/**
@@ -103,6 +105,7 @@ umi:
fastp:
- conf/modules/trimming.config
- modules/nf-core/fastp/**
+ - modules/nf-core/mosdepth/**
- tests/csv/3.0/fastq_single.csv
- tests/test_fastp.yml
@@ -112,6 +115,7 @@ fastp:
bwamem:
- conf/modules/aligner.config
- modules/nf-core/bwa/mem/**
+ - modules/nf-core/mosdepth/**
- subworkflows/local/fastq_align_bwamem_mem2_dragmap_sentieon/**
- tests/csv/3.0/fastq_single.csv
- tests/test_aligner_bwamem.yml
@@ -120,6 +124,7 @@ bwamem:
bwamem2:
- conf/modules/aligner.config
- modules/nf-core/bwamem2/mem/**
+ - modules/nf-core/mosdepth/**
- subworkflows/local/fastq_align_bwamem_mem2_dragmap_sentieon/**
- tests/csv/3.0/fastq_single.csv
- tests/test_aligner_bwamem2.yml
@@ -128,6 +133,7 @@ bwamem2:
dragmap:
- conf/modules/aligner.config
- modules/nf-core/dragmap/align/**
+ - modules/nf-core/mosdepth/**
- subworkflows/local/fastq_align_bwamem_mem2_dragmap_sentieon/**
- tests/csv/3.0/fastq_single.csv
- tests/test_aligner_dragmap.yml
@@ -174,6 +180,7 @@ prepare_recalibration:
- conf/modules/prepare_recalibration.config
- modules/nf-core/gatk4/baserecalibrator/**
- modules/nf-core/gatk4/gatherbqsrreports/**
+ - modules/nf-core/mosdepth/**
- modules/nf-core/samtools/convert/**
- subworkflows/local/bam_baserecalibrator/**
- tests/csv/3.0/mapped_single_bam.csv
@@ -188,6 +195,7 @@ recalibrate:
- modules/nf-core/samtools/convert/**
- modules/nf-core/samtools/index/**
- modules/nf-core/samtools/merge/**
+ - modules/nf-core/mosdepth/**
- subworkflows/local/bam_applybqsr/**
- subworkflows/local/cram_merge_index_samtools/**
- tests/csv/3.0/prepare_recalibration_single_bam.csv
@@ -201,6 +209,7 @@ intervals:
- modules/local/build_intervals/**
- modules/local/create_intervals_bed/**
- modules/nf-core/gatk4/intervallisttobed/**
+ - modules/nf-core/mosdepth/**
- modules/nf-core/tabix/bgziptabix/**
- subworkflows/local/prepare_intervals/**
- tests/csv/3.0/fastq_single.csv
@@ -215,6 +224,7 @@ gatk4spark:
- modules/nf-core/gatk4spark/baserecalibrator/**
- modules/nf-core/gatk4/estimatelibrarycomplexity/**
- modules/nf-core/gatk4spark/markduplicates/**
+ - modules/nf-core/mosdepth/**
- subworkflows/local/bam_applybqsr_spark/**
- subworkflows/local/bam_baserecalibrator_spark/**
- subworkflows/local/bam_markduplicates_spark/**
@@ -229,6 +239,7 @@ cnvkit:
- modules/nf-core/cnvkit/antitarget/**
- modules/nf-core/cnvkit/batch/**
- modules/nf-core/cnvkit/reference/**
+ - modules/nf-core/mosdepth/**
- subworkflows/local/bam_variant_calling_cnvkit/**
- subworkflows/local/bam_variant_calling_germline_all/**
- subworkflows/local/bam_variant_calling_somatic_all/**
@@ -249,6 +260,7 @@ controlfreec:
- modules/nf-core/controlfreec/freec2bed/**
- modules/nf-core/controlfreec/freec2circos/**
- modules/nf-core/controlfreec/makegraph2/**
+ - modules/nf-core/mosdepth/**
- modules/nf-core/samtools/mpileup/**
- subworkflows/local/bam_variant_calling_mpileup/**
- subworkflows/local/bam_variant_calling_somatic_all/**
@@ -264,6 +276,7 @@ deepvariant:
- conf/modules/deepvariant.config
- modules/nf-core/deepvariant/**
- modules/nf-core/gatk4/mergevcfs/**
+ - modules/nf-core/mosdepth/**
- modules/nf-core/tabix/tabix/**
- subworkflows/local/bam_variant_calling_deepvariant/**
- subworkflows/local/bam_variant_calling_germline_all/**
@@ -276,6 +289,7 @@ freebayes:
- modules/nf-core/bcftools/sort/**
- modules/nf-core/freebayes/**
- modules/nf-core/gatk4/mergevcfs/**
+ - modules/nf-core/mosdepth/**
- modules/nf-core/tabix/tabix/**
- subworkflows/local/bam_variant_calling_freebayes/**
- subworkflows/local/bam_variant_calling_germline_all/**
@@ -293,6 +307,7 @@ haplotypecaller:
- modules/nf-core/gatk4/filtervarianttranches/**
- modules/nf-core/gatk4/haplotypecaller/**
- modules/nf-core/gatk4/mergevcfs/**
+ - modules/nf-core/mosdepth/**
- modules/nf-core/samtools/index/**
- modules/nf-core/samtools/merge/**
- subworkflows/local/bam_merge_index_samtools/**
@@ -379,6 +394,7 @@ joint_germline:
- modules/nf-core/gatk4/haplotypecaller/**
- modules/nf-core/gatk4/mergevcfs/**
- modules/nf-core/gatk4/variantrecalibrator/**
+ - modules/nf-core/mosdepth/**
- modules/nf-core/samtools/index/**
- modules/nf-core/samtools/merge/**
- subworkflows/local/bam_joint_calling_germline_gatk/**
@@ -418,6 +434,7 @@ manta:
- modules/nf-core/manta/germline/**
- modules/nf-core/manta/somatic/**
- modules/nf-core/manta/tumoronly/**
+ - modules/nf-core/mosdepth/**
- subworkflows/local/bam_variant_calling_germline_all/**
- subworkflows/local/bam_variant_calling_germline_manta/**
- subworkflows/local/bam_variant_calling_somatic_all/**
@@ -433,6 +450,7 @@ manta:
mpileup:
- conf/modules/mpileup.config
- modules/nf-core/cat/cat/**
+ - modules/nf-core/mosdepth/**
- modules/nf-core/samtools/mpileup/**
- subworkflows/local/bam_variant_calling_germline_all/**
- subworkflows/local/bam_variant_calling_mpileup/**
@@ -447,6 +465,7 @@ msisensorpro:
- conf/modules/msisensorpro.config
- modules/nf-core/msisensorpro/msi_somatic/**
- modules/nf-core/msisensorpro/scan/**
+ - modules/nf-core/mosdepth/**
- subworkflows/local/bam_variant_calling_somatic_all/**
- tests/csv/3.0/recalibrated_somatic.csv
- tests/test_msisensorpro.yml
@@ -462,6 +481,7 @@ mutect2:
- modules/nf-core/gatk4/mergemutectstats/**
- modules/nf-core/gatk4/mergevcfs/**
- modules/nf-core/gatk4/mutect2/**
+ - modules/nf-core/mosdepth/**
- subworkflows/local/bam_variant_calling_somatic_all/**
- subworkflows/local/bam_variant_calling_somatic_mutect2/**
- subworkflows/local/bam_variant_calling_tumor_only_all/**
@@ -473,6 +493,7 @@ mutect2:
strelka:
- conf/modules/strelka.config
- modules/nf-core/gatk4/mergevcfs/**
+ - modules/nf-core/mosdepth/**
- modules/nf-core/strelka/germline/**
- modules/nf-core/strelka/somatic/**
- subworkflows/local/bam_variant_calling_germline_all/**
@@ -492,6 +513,7 @@ strelka_bp:
- conf/modules/strelka.config
- modules/nf-core/gatk4/mergevcfs/**
- modules/nf-core/manta/somatic/**
+ - modules/nf-core/mosdepth/**
- modules/nf-core/strelka/somatic/**
- subworkflows/local/bam_variant_calling_germline_all/**
- subworkflows/local/bam_variant_calling_somatic_all/**
@@ -505,6 +527,7 @@ strelka_bp:
tiddit:
- conf/modules/tiddit.config
- modules/nf-core/svdb/merge/**.nf
+ - modules/nf-core/mosdepth/**
- modules/nf-core/tabix/bgziptabix/**
- modules/nf-core/tiddit/sv/**
- subworkflows/local/bam_variant_calling_germline_all/**
diff --git a/tests/main.nf.test b/tests/main.nf.test
index ad9209ab88..53e3dc0ca6 100644
--- a/tests/main.nf.test
+++ b/tests/main.nf.test
@@ -14,8 +14,6 @@ nextflow_pipeline {
max_memory = '6.GB'
max_time = '6.h'
input = "$projectDir/tests/csv/3.0/fastq_pair.csv"
- validationSchemaIgnoreParams = 'test_data_base,test_data,genomes'
- use_gatk_spark = false
}
}
@@ -25,5 +23,4 @@ nextflow_pipeline {
)
}
}
-
}
diff --git a/tests/test_aligner_bwamem.yml b/tests/test_aligner_bwamem.yml
index ea51c0ccd5..ccd81021ef 100644
--- a/tests/test_aligner_bwamem.yml
+++ b/tests/test_aligner_bwamem.yml
@@ -1,5 +1,5 @@
- name: Run bwamem
- command: nextflow run main.nf -profile test_cache --aligner bwa-mem --save_reference --outdir results
+ command: nextflow run main.nf -profile test --aligner bwa-mem --save_reference --outdir results
tags:
- aligner
- bwamem
@@ -32,49 +32,31 @@
md5sum: 8569fbdb2c98c6fb16dfa73d8eacb070
- path: results/reference/bwa/genome.sa
md5sum: e7cff62b919448a3a3d0fe4aaf427594
- - path: results/reference/dbsnp/dbsnp_146.hg38.vcf.gz.tbi
- # conda changes md5sums for test
- - path: results/reference/dict/genome.dict
- md5sum: 2433fe2ba31257337bf4c4bd4cb8da15
- - path: results/reference/fai/genome.fasta.fai
- md5sum: 3520cd30e1b100e55f578db9c855f685
- path: results/reference/intervals/chr22_1-40001.bed
md5sum: 87a15eb9c2ff20ccd5cd8735a28708f7
- path: results/reference/intervals/chr22_1-40001.bed.gz
md5sum: d3341fa28986c40b24fcc10a079dbb80
- path: results/reference/intervals/genome.bed
md5sum: a87dc7d20ebca626f65cc16ff6c97a3e
- - path: results/reference/known_indels/mills_and_1000G.indels.vcf.gz.tbi
- # conda changes md5sums for test
- path: results/reports/fastqc/test-test_L1
- path: results/reports/markduplicates/test/test.md.cram.metrics
contains: ["test 17094 1534 168 1046782 12429 197 0 0.635998", "1.0 0.999991 1171"]
- path: results/reports/mosdepth/test/test.md.mosdepth.global.dist.txt
- md5sum: b61e1acee11a6ddf7ce3232a5948a6a0
- path: results/reports/mosdepth/test/test.md.mosdepth.region.dist.txt
- md5sum: 1a382f98d488d2ae3df83a0d87caafc1
- path: results/reports/mosdepth/test/test.md.mosdepth.summary.txt
- md5sum: 839108358878ada89e1eaddf6e0541ba
- path: results/reports/mosdepth/test/test.md.regions.bed.gz
- md5sum: 0aaee6da65050bedcd40b9fbf0622873
- path: results/reports/mosdepth/test/test.md.regions.bed.gz.csi
- md5sum: 544e02fcca548749a0af758d0a2df352
- path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt
- md5sum: b61e1acee11a6ddf7ce3232a5948a6a0
- path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt
- md5sum: 1a382f98d488d2ae3df83a0d87caafc1
- path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt
- md5sum: 839108358878ada89e1eaddf6e0541ba
- path: results/reports/mosdepth/test/test.recal.regions.bed.gz
- md5sum: 0aaee6da65050bedcd40b9fbf0622873
- path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi
- md5sum: 544e02fcca548749a0af758d0a2df352
- path: results/reports/samtools/test/test.md.cram.stats
# conda changes md5sums for test
- path: results/reports/samtools/test/test.recal.cram.stats
# conda changes md5sums for test
- name: Build only index with bwa
- command: nextflow run main.nf -profile test_cache --build_only_index --input false --outdir results
+ command: nextflow run main.nf -profile test --build_only_index --input false --outdir results
tags:
- aligner
- build_only_index
@@ -91,17 +73,9 @@
md5sum: 8569fbdb2c98c6fb16dfa73d8eacb070
- path: results/reference/bwa/genome.sa
md5sum: e7cff62b919448a3a3d0fe4aaf427594
- - path: results/reference/dbsnp/dbsnp_146.hg38.vcf.gz.tbi
- # conda changes md5sums for test
- - path: results/reference/dict/genome.dict
- md5sum: 2433fe2ba31257337bf4c4bd4cb8da15
- - path: results/reference/fai/genome.fasta.fai
- md5sum: 3520cd30e1b100e55f578db9c855f685
- path: results/reference/intervals/chr22_1-40001.bed
md5sum: 87a15eb9c2ff20ccd5cd8735a28708f7
- path: results/reference/intervals/chr22_1-40001.bed.gz
md5sum: d3341fa28986c40b24fcc10a079dbb80
- path: results/reference/intervals/genome.bed
md5sum: a87dc7d20ebca626f65cc16ff6c97a3e
- - path: results/reference/known_indels/mills_and_1000G.indels.vcf.gz.tbi
- # conda changes md5sums for test
diff --git a/tests/test_aligner_bwamem2.yml b/tests/test_aligner_bwamem2.yml
index 17760a558b..be19c08df6 100644
--- a/tests/test_aligner_bwamem2.yml
+++ b/tests/test_aligner_bwamem2.yml
@@ -1,5 +1,5 @@
- name: Run bwamem2
- command: nextflow run main.nf -profile test_cache --aligner bwa-mem2 --save_reference --outdir results
+ command: nextflow run main.nf -profile test --aligner bwa-mem2 --save_reference --outdir results
tags:
- aligner
- bwamem2
@@ -32,49 +32,31 @@
md5sum: cd4bdf496eab05228a50c45ee43c1ed0
- path: results/reference/bwamem2/genome.fasta.pac
md5sum: 8569fbdb2c98c6fb16dfa73d8eacb070
- - path: results/reference/dbsnp/dbsnp_146.hg38.vcf.gz.tbi
- # conda changes md5sums for test
- - path: results/reference/dict/genome.dict
- md5sum: 2433fe2ba31257337bf4c4bd4cb8da15
- - path: results/reference/fai/genome.fasta.fai
- md5sum: 3520cd30e1b100e55f578db9c855f685
- path: results/reference/intervals/chr22_1-40001.bed
md5sum: 87a15eb9c2ff20ccd5cd8735a28708f7
- path: results/reference/intervals/chr22_1-40001.bed.gz
md5sum: d3341fa28986c40b24fcc10a079dbb80
- path: results/reference/intervals/genome.bed
md5sum: a87dc7d20ebca626f65cc16ff6c97a3e
- - path: results/reference/known_indels/mills_and_1000G.indels.vcf.gz.tbi
- # conda changes md5sums for test
- path: results/reports/fastqc/test-test_L1
- path: results/reports/markduplicates/test/test.md.cram.metrics
contains: ["test 17094 1534 168 1046782 12429 197 0 0.635998", "1.0 0.999991 1171"]
- path: results/reports/mosdepth/test/test.md.mosdepth.global.dist.txt
- md5sum: b61e1acee11a6ddf7ce3232a5948a6a0
- path: results/reports/mosdepth/test/test.md.mosdepth.region.dist.txt
- md5sum: 1a382f98d488d2ae3df83a0d87caafc1
- path: results/reports/mosdepth/test/test.md.mosdepth.summary.txt
- md5sum: 839108358878ada89e1eaddf6e0541ba
- path: results/reports/mosdepth/test/test.md.regions.bed.gz
- md5sum: 0aaee6da65050bedcd40b9fbf0622873
- path: results/reports/mosdepth/test/test.md.regions.bed.gz.csi
- md5sum: 544e02fcca548749a0af758d0a2df352
- path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt
- md5sum: b61e1acee11a6ddf7ce3232a5948a6a0
- path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt
- md5sum: 1a382f98d488d2ae3df83a0d87caafc1
- path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt
- md5sum: 839108358878ada89e1eaddf6e0541ba
- path: results/reports/mosdepth/test/test.recal.regions.bed.gz
- md5sum: 0aaee6da65050bedcd40b9fbf0622873
- path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi
- md5sum: 544e02fcca548749a0af758d0a2df352
- path: results/reports/samtools/test/test.md.cram.stats
# conda changes md5sums for test
- path: results/reports/samtools/test/test.recal.cram.stats
# conda changes md5sums for test
- name: Build only index with bwa-mem2
- command: nextflow run main.nf -profile test_cache --build_only_index --aligner bwa-mem2 --input false --outdir results
+ command: nextflow run main.nf -profile test --build_only_index --aligner bwa-mem2 --input false --outdir results
tags:
- aligner
- build_only_index
@@ -91,17 +73,9 @@
md5sum: cd4bdf496eab05228a50c45ee43c1ed0
- path: results/reference/bwamem2/genome.fasta.pac
md5sum: 8569fbdb2c98c6fb16dfa73d8eacb070
- - path: results/reference/dbsnp/dbsnp_146.hg38.vcf.gz.tbi
- # conda changes md5sums for test
- - path: results/reference/dict/genome.dict
- md5sum: 2433fe2ba31257337bf4c4bd4cb8da15
- - path: results/reference/fai/genome.fasta.fai
- md5sum: 3520cd30e1b100e55f578db9c855f685
- path: results/reference/intervals/chr22_1-40001.bed
md5sum: 87a15eb9c2ff20ccd5cd8735a28708f7
- path: results/reference/intervals/chr22_1-40001.bed.gz
md5sum: d3341fa28986c40b24fcc10a079dbb80
- path: results/reference/intervals/genome.bed
md5sum: a87dc7d20ebca626f65cc16ff6c97a3e
- - path: results/reference/known_indels/mills_and_1000G.indels.vcf.gz.tbi
- # conda changes md5sums for test
diff --git a/tests/test_aligner_dragmap.yml b/tests/test_aligner_dragmap.yml
index a4960d8e02..6f38538926 100644
--- a/tests/test_aligner_dragmap.yml
+++ b/tests/test_aligner_dragmap.yml
@@ -1,5 +1,5 @@
- name: Run dragmap
- command: nextflow run main.nf -profile test_cache --aligner dragmap --save_reference --outdir results
+ command: nextflow run main.nf -profile test --aligner dragmap --save_reference --outdir results
tags:
- aligner
- dragmap
@@ -22,10 +22,6 @@
# binary changes md5sums on reruns
- path: results/preprocessing/recalibrated/test/test.recal.cram.crai
# binary changes md5sums on reruns
- - path: results/reference/dbsnp/dbsnp_146.hg38.vcf.gz.tbi
- # conda changes md5sums for test
- - path: results/reference/dict/genome.dict
- md5sum: 2433fe2ba31257337bf4c4bd4cb8da15
- path: results/reference/dragmap/hash_table.cfg
contains:
[
@@ -49,45 +45,31 @@
md5sum: 294939f1f80aa7f4a70b9b537e4c0f21
- path: results/reference/dragmap/str_table.bin
md5sum: 45f7818c4a10fdeed04db7a34b5f9ff1
- - path: results/reference/fai/genome.fasta.fai
- md5sum: 3520cd30e1b100e55f578db9c855f685
- path: results/reference/intervals/chr22_1-40001.bed
md5sum: 87a15eb9c2ff20ccd5cd8735a28708f7
- path: results/reference/intervals/chr22_1-40001.bed.gz
md5sum: d3341fa28986c40b24fcc10a079dbb80
- path: results/reference/intervals/genome.bed
md5sum: a87dc7d20ebca626f65cc16ff6c97a3e
- - path: results/reference/known_indels/mills_and_1000G.indels.vcf.gz.tbi
- # conda changes md5sums for test
- path: results/reports/fastqc/test-test_L1
- path: results/reports/markduplicates/test/test.md.cram.metrics
contains: ["LB0 27214 1086 322 1037558 20017 100 0 0.687981"]
- path: results/reports/mosdepth/test/test.md.mosdepth.global.dist.txt
- md5sum: b0d7d5de1e00132bb5b47e1b3d90d944
- path: results/reports/mosdepth/test/test.md.mosdepth.region.dist.txt
- md5sum: 02b88d7ec0ca8ff23ba688c35939fa05
- path: results/reports/mosdepth/test/test.md.mosdepth.summary.txt
- md5sum: 1792d98676f597f755749f4286c5102d
- path: results/reports/mosdepth/test/test.md.regions.bed.gz
- md5sum: 590119568d091ce3a88f7fe4f43f24ff
- path: results/reports/mosdepth/test/test.md.regions.bed.gz.csi
- md5sum: 2e7fe057ead0622e6a2a6b0ed1832315
- path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt
- md5sum: b0d7d5de1e00132bb5b47e1b3d90d944
- path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt
- md5sum: 02b88d7ec0ca8ff23ba688c35939fa05
- path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt
- md5sum: 1792d98676f597f755749f4286c5102d
- path: results/reports/mosdepth/test/test.recal.regions.bed.gz
- md5sum: 590119568d091ce3a88f7fe4f43f24ff
- path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi
- md5sum: 2e7fe057ead0622e6a2a6b0ed1832315
- path: results/reports/samtools/test/test.md.cram.stats
# conda changes md5sums for test
- path: results/reports/samtools/test/test.recal.cram.stats
# conda changes md5sums for test
- name: Build only index with dragmap
- command: nextflow run main.nf -profile test_cache --build_only_index --aligner dragmap --input false --outdir results
+ command: nextflow run main.nf -profile test --build_only_index --aligner dragmap --input false --outdir results
tags:
- aligner
- build_only_index
@@ -117,17 +99,9 @@
md5sum: 294939f1f80aa7f4a70b9b537e4c0f21
- path: results/reference/dragmap/str_table.bin
md5sum: 45f7818c4a10fdeed04db7a34b5f9ff1
- - path: results/reference/dbsnp/dbsnp_146.hg38.vcf.gz.tbi
- # conda changes md5sums for test
- - path: results/reference/dict/genome.dict
- md5sum: 2433fe2ba31257337bf4c4bd4cb8da15
- - path: results/reference/fai/genome.fasta.fai
- md5sum: 3520cd30e1b100e55f578db9c855f685
- path: results/reference/intervals/chr22_1-40001.bed
md5sum: 87a15eb9c2ff20ccd5cd8735a28708f7
- path: results/reference/intervals/chr22_1-40001.bed.gz
md5sum: d3341fa28986c40b24fcc10a079dbb80
- path: results/reference/intervals/genome.bed
md5sum: a87dc7d20ebca626f65cc16ff6c97a3e
- - path: results/reference/known_indels/mills_and_1000G.indels.vcf.gz.tbi
- # conda changes md5sums for test
diff --git a/tests/test_alignment_to_fastq.yml b/tests/test_alignment_to_fastq.yml
index 6077b745d4..bc7a3e5057 100644
--- a/tests/test_alignment_to_fastq.yml
+++ b/tests/test_alignment_to_fastq.yml
@@ -1,5 +1,5 @@
- name: Run alignment to fastq and then remap on bam files
- command: nextflow run main.nf -profile test_cache,alignment_to_fastq --outdir results
+ command: nextflow run main.nf -profile test,alignment_to_fastq --outdir results
tags:
- alignment_to_fastq
- input_bam
@@ -25,25 +25,15 @@
- path: results/reports/markduplicates/test/test.md.cram.metrics
contains: ["test 0 2820 2 2 0 828 0 0.293617 3807", "1.0 0.999986 1178 1178", "2.0 1.47674 800 800", "100.0 1.911145 0 0"]
- path: results/reports/mosdepth/test/test.md.mosdepth.global.dist.txt
- md5sum: 9cb9b181119256ed17a77dcf44d58285
- path: results/reports/mosdepth/test/test.md.mosdepth.region.dist.txt
- md5sum: 75e1ce7e55af51f4985fa91654a5ea2d
- path: results/reports/mosdepth/test/test.md.mosdepth.summary.txt
- md5sum: dbe376360e437c89190139ef0ae6769a
- path: results/reports/mosdepth/test/test.md.regions.bed.gz
- md5sum: d9b53915d473710ff0260a0ff694fd32
- path: results/reports/mosdepth/test/test.md.regions.bed.gz.csi
- md5sum: d0713716f63ac573f4a3385733e9a537
- path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt
- md5sum: 9cb9b181119256ed17a77dcf44d58285
- path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt
- md5sum: 75e1ce7e55af51f4985fa91654a5ea2d
- path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt
- md5sum: dbe376360e437c89190139ef0ae6769a
- path: results/reports/mosdepth/test/test.recal.regions.bed.gz
- md5sum: d9b53915d473710ff0260a0ff694fd32
- path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi
- md5sum: d0713716f63ac573f4a3385733e9a537
- path: results/reports/samtools/test/test.md.cram.stats
# conda changes md5sums for test
- path: results/reports/samtools/test/test.recal.cram.stats
diff --git a/tests/test_annotation_bcfann.yml b/tests/test_annotation_bcfann.yml
index 5b9546b961..99ac781d8e 100644
--- a/tests/test_annotation_bcfann.yml
+++ b/tests/test_annotation_bcfann.yml
@@ -1,5 +1,5 @@
- name: Run bcfann
- command: nextflow run main.nf -profile test_cache,annotation --tools bcfann --outdir results
+ command: nextflow run main.nf -profile test,annotation --tools bcfann --outdir results
tags:
- annotation
- bcfann
diff --git a/tests/test_annotation_cache.yml b/tests/test_annotation_cache.yml
index fd84fb47e4..290169d32d 100644
--- a/tests/test_annotation_cache.yml
+++ b/tests/test_annotation_cache.yml
@@ -1,5 +1,5 @@
- name: Only download annotation cache
- command: nextflow run main.nf -profile test_cache,annotation --tools merge --download_cache --input false --build_only_index --outdir results
+ command: nextflow run main.nf -profile test,annotation --tools merge --download_cache --input false --build_only_index --outdir results
tags:
- annotation
- cache
@@ -13,7 +13,7 @@
should_exist: false
- name: Fail to locate VEP cache
- command: nextflow run main.nf -profile test_cache,annotation --vep_cache s3://annotation-cache/vep_cache/ --vep_cache_version 1 --tools vep --input false --build_only_index --outdir results
+ command: nextflow run main.nf -profile test,annotation --vep_cache s3://annotation-cache/vep_cache/ --vep_cache_version 1 --tools vep --input false --build_only_index --outdir results
tags:
- annotation
- cache
@@ -21,7 +21,7 @@
exit_code: 1
- name: Fail to locate snpEff cache
- command: nextflow run main.nf -profile test_cache,annotation --snpeff_cache s3://annotation-cache/snpeff_cache/ --snpeff_genome na --tools snpeff --input false --build_only_index --outdir results
+ command: nextflow run main.nf -profile test,annotation --snpeff_cache s3://annotation-cache/snpeff_cache/ --snpeff_genome na --tools snpeff --input false --build_only_index --outdir results
tags:
- annotation
- cache
diff --git a/tests/test_annotation_merge.yml b/tests/test_annotation_merge.yml
index 21351f1cfc..7c39948743 100644
--- a/tests/test_annotation_merge.yml
+++ b/tests/test_annotation_merge.yml
@@ -1,5 +1,5 @@
- name: Run snpEff followed by VEP
- command: nextflow run main.nf -profile test_cache,annotation --tools merge --outdir results --download_cache
+ command: nextflow run main.nf -profile test,annotation --tools merge --outdir results --download_cache
tags:
- annotation
- merge
@@ -28,7 +28,7 @@
- path: results/reports/EnsemblVEP/test/test_VEP.ann.summary.html
should_exist: false
- name: Run VEP and snpEff followed by VEP
- command: nextflow run main.nf -profile test_cache,annotation --tools merge,snpeff,vep --outdir results --download_cache
+ command: nextflow run main.nf -profile test,annotation --tools merge,snpeff,vep --outdir results --download_cache
tags:
- annotation
- merge
diff --git a/tests/test_annotation_snpeff.yml b/tests/test_annotation_snpeff.yml
index d6ce2ee48d..5ad71d0664 100644
--- a/tests/test_annotation_snpeff.yml
+++ b/tests/test_annotation_snpeff.yml
@@ -1,5 +1,5 @@
- name: Run snpEff
- command: nextflow run main.nf -profile test_cache,annotation --tools snpeff --outdir results --download_cache
+ command: nextflow run main.nf -profile test,annotation --tools snpeff --outdir results --download_cache
tags:
- annotation
- snpeff
diff --git a/tests/test_annotation_vep.yml b/tests/test_annotation_vep.yml
index 176c85020c..c8c16747b2 100644
--- a/tests/test_annotation_vep.yml
+++ b/tests/test_annotation_vep.yml
@@ -1,5 +1,5 @@
- name: Run VEP
- command: nextflow run main.nf -profile test_cache,annotation --tools vep --outdir results --download_cache
+ command: nextflow run main.nf -profile test,annotation --tools vep --outdir results --download_cache
tags:
- annotation
- vep
@@ -12,7 +12,7 @@
- path: results/reports/EnsemblVEP/test/test_VEP.ann.summary.html
contains: ["test.vcf.gz| Output file | test_VEP.ann.vcf.gz |
"]
- name: Run VEP with fasta
- command: nextflow run main.nf -profile test_cache,annotation --tools vep --vep_include_fasta --outdir results --download_cache
+ command: nextflow run main.nf -profile test,annotation --tools vep --vep_include_fasta --outdir results --download_cache
tags:
- annotation
- vep
diff --git a/tests/test_cnvkit.yml b/tests/test_cnvkit.yml
index 8e9017c70b..43828e540e 100644
--- a/tests/test_cnvkit.yml
+++ b/tests/test_cnvkit.yml
@@ -1,5 +1,5 @@
- name: Run variant calling on somatic samples with cnvkit
- command: nextflow run main.nf -profile test_cache,tools_somatic --tools cnvkit --outdir results
+ command: nextflow run main.nf -profile test,tools_somatic --tools cnvkit --outdir results
tags:
- cnvkit
- copy_number_calling
@@ -58,31 +58,21 @@
- path: results/cnvkit
should_exist: false
- path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.global.dist.txt
- md5sum: 69e29702ef01fd8f6c7a5468fc35a16a
- path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.region.dist.txt
- md5sum: 6ec49cd7d510c2eb3d9d90fdb79b783a
- path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.summary.txt
- md5sum: 103098d0bf76ed82d2b87d5f242b099a
- path: results/reports/mosdepth/sample3/sample3.recal.regions.bed.gz
- md5sum: b5888cf7395c57d39879a5faa6159eb3
- path: results/reports/mosdepth/sample3/sample3.recal.regions.bed.gz.csi
- md5sum: 9cb0ad7039a3b703d16ca7d5b835c0ee
- path: results/reports/samtools/sample3/sample3.recal.cram.stats
# conda changes md5sums for test
- path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.global.dist.txt
- md5sum: f2dcd00a64947c49e8e4b93c2f4fbf27
- path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.region.dist.txt
- md5sum: 39005ffaac22871ffaaf19656fe69c5b
- path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.summary.txt
- md5sum: 68d4b98f17361fddf73052ead34fa370
- path: results/reports/mosdepth/sample4/sample4.recal.regions.bed.gz
- md5sum: 2819e995eafded35f53328c4ec19ba58
- path: results/reports/mosdepth/sample4/sample4.recal.regions.bed.gz.csi
- md5sum: 393c2749068304d8545b501b9d4658e4
- path: results/reports/samtools/sample4/sample4.recal.cram.stats
# conda changes md5sums for test
- name: Run variant calling on tumor_only sample with cnvkit
- command: nextflow run main.nf -profile test_cache,tools_tumoronly --tools cnvkit --outdir results
+ command: nextflow run main.nf -profile test,tools_tumoronly --tools cnvkit --outdir results
tags:
- cnvkit
- copy_number_calling
@@ -113,18 +103,13 @@
- path: results/cnvkit
should_exist: false
- path: results/reports/mosdepth/sample2/sample2.recal.mosdepth.global.dist.txt
- md5sum: f2dcd00a64947c49e8e4b93c2f4fbf27
- path: results/reports/mosdepth/sample2/sample2.recal.mosdepth.region.dist.txt
- md5sum: 39005ffaac22871ffaaf19656fe69c5b
- path: results/reports/mosdepth/sample2/sample2.recal.mosdepth.summary.txt
- md5sum: 68d4b98f17361fddf73052ead34fa370
- path: results/reports/mosdepth/sample2/sample2.recal.regions.bed.gz
- md5sum: 2819e995eafded35f53328c4ec19ba58
- path: results/reports/mosdepth/sample2/sample2.recal.regions.bed.gz.csi
- md5sum: 393c2749068304d8545b501b9d4658e4
- path: results/reports/samtools/sample2/sample2.recal.cram.stats
- name: Run variant calling on germline sample with cnvkit
- command: nextflow run main.nf -profile test_cache,tools_germline --tools cnvkit --outdir results
+ command: nextflow run main.nf -profile test,tools_germline --tools cnvkit --outdir results
tags:
- cnvkit
- copy_number_calling
@@ -157,18 +142,13 @@
- path: results/cnvkit
should_exist: false
- path: results/reports/mosdepth/sample1/sample1.recal.mosdepth.global.dist.txt
- md5sum: 69e29702ef01fd8f6c7a5468fc35a16a
- path: results/reports/mosdepth/sample1/sample1.recal.mosdepth.region.dist.txt
- md5sum: 6ec49cd7d510c2eb3d9d90fdb79b783a
- path: results/reports/mosdepth/sample1/sample1.recal.mosdepth.summary.txt
- md5sum: 103098d0bf76ed82d2b87d5f242b099a
- path: results/reports/mosdepth/sample1/sample1.recal.regions.bed.gz
- md5sum: b5888cf7395c57d39879a5faa6159eb3
- path: results/reports/mosdepth/sample1/sample1.recal.regions.bed.gz.csi
- md5sum: 9cb0ad7039a3b703d16ca7d5b835c0ee
- path: results/reports/samtools/sample1/sample1.recal.cram.stats
- name: Run variant calling on somatic samples with cnvkit and skip variant calling on matched normal
- command: nextflow run main.nf -profile test_cache,tools_somatic --tools cnvkit --only_paired_variant_calling --outdir results
+ command: nextflow run main.nf -profile test,tools_somatic --tools cnvkit --only_paired_variant_calling --outdir results
tags:
- cnvkit
- somatic
@@ -203,26 +183,16 @@
- path: results/variant_calling/cnvkit/sample4_vs_sample3/test2.paired_end.recalibrated.sorted.targetcoverage.cnn
md5sum: b4a49faf170e436ec32dcc21ccc3ce8f
- path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.global.dist.txt
- md5sum: 69e29702ef01fd8f6c7a5468fc35a16a
- path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.region.dist.txt
- md5sum: 6ec49cd7d510c2eb3d9d90fdb79b783a
- path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.summary.txt
- md5sum: 103098d0bf76ed82d2b87d5f242b099a
- path: results/reports/mosdepth/sample3/sample3.recal.regions.bed.gz
- md5sum: b5888cf7395c57d39879a5faa6159eb3
- path: results/reports/mosdepth/sample3/sample3.recal.regions.bed.gz.csi
- md5sum: 9cb0ad7039a3b703d16ca7d5b835c0ee
- path: results/reports/samtools/sample3/sample3.recal.cram.stats
# conda changes md5sums for test
- path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.global.dist.txt
- md5sum: f2dcd00a64947c49e8e4b93c2f4fbf27
- path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.region.dist.txt
- md5sum: 39005ffaac22871ffaaf19656fe69c5b
- path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.summary.txt
- md5sum: 68d4b98f17361fddf73052ead34fa370
- path: results/reports/mosdepth/sample4/sample4.recal.regions.bed.gz
- md5sum: 2819e995eafded35f53328c4ec19ba58
- path: results/reports/mosdepth/sample4/sample4.recal.regions.bed.gz.csi
- md5sum: 393c2749068304d8545b501b9d4658e4
- path: results/reports/samtools/sample4/sample4.recal.cram.stats
# conda changes md5sums for test
diff --git a/tests/test_concat_germline_vcfs.yml b/tests/test_concat_germline_vcfs.yml
index 8a32231ac8..97a2453fbc 100644
--- a/tests/test_concat_germline_vcfs.yml
+++ b/tests/test_concat_germline_vcfs.yml
@@ -1,5 +1,5 @@
- name: Run all germline variant callers and check for existence of concatenated vcf-files
- command: nextflow run main.nf -profile test_cache --input ./tests/csv/3.0/mapped_joint_bam.csv --concatenate_vcfs --tools deepvariant,freebayes,haplotypecaller,manta,mpileup,strelka,tiddit --step variant_calling --outdir results
+ command: nextflow run main.nf -profile test --input ./tests/csv/3.0/mapped_joint_bam.csv --concatenate_vcfs --tools deepvariant,freebayes,haplotypecaller,manta,mpileup,strelka,tiddit --step variant_calling --outdir results
tags:
- concatenate_vcfs
files:
diff --git a/tests/test_controlfreec.yml b/tests/test_controlfreec.yml
index 4d938351f4..d72b67ed27 100644
--- a/tests/test_controlfreec.yml
+++ b/tests/test_controlfreec.yml
@@ -1,5 +1,5 @@
- name: Run variant calling on somatic samples with controlfreec
- command: nextflow run main.nf -profile test_cache,tools_somatic --tools controlfreec --outdir results
+ command: nextflow run main.nf -profile test,tools_somatic --tools controlfreec --outdir results
tags:
- controlfreec
- somatic
@@ -51,31 +51,21 @@
- path: results/cnvkit
should_exist: false
- path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.global.dist.txt
- md5sum: 69e29702ef01fd8f6c7a5468fc35a16a
- path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.region.dist.txt
- md5sum: 6ec49cd7d510c2eb3d9d90fdb79b783a
- path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.summary.txt
- md5sum: 103098d0bf76ed82d2b87d5f242b099a
- path: results/reports/mosdepth/sample3/sample3.recal.regions.bed.gz
- md5sum: b5888cf7395c57d39879a5faa6159eb3
- path: results/reports/mosdepth/sample3/sample3.recal.regions.bed.gz.csi
- md5sum: 9cb0ad7039a3b703d16ca7d5b835c0ee
- path: results/reports/samtools/sample3/sample3.recal.cram.stats
# conda changes md5sums for test
- path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.global.dist.txt
- md5sum: f2dcd00a64947c49e8e4b93c2f4fbf27
- path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.region.dist.txt
- md5sum: 39005ffaac22871ffaaf19656fe69c5b
- path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.summary.txt
- md5sum: 68d4b98f17361fddf73052ead34fa370
- path: results/reports/mosdepth/sample4/sample4.recal.regions.bed.gz
- md5sum: 2819e995eafded35f53328c4ec19ba58
- path: results/reports/mosdepth/sample4/sample4.recal.regions.bed.gz.csi
- md5sum: 393c2749068304d8545b501b9d4658e4
- path: results/reports/samtools/sample4/sample4.recal.cram.stats
# conda changes md5sums for test
- name: Run variant calling on somatic samples with controlfreec without intervals
- command: nextflow run main.nf -profile test_cache,tools_somatic --tools controlfreec --no_intervals -stub-run --outdir results
+ command: nextflow run main.nf -profile test,tools_somatic --tools controlfreec --no_intervals -stub-run --outdir results
tags:
- controlfreec
- no_intervals
@@ -127,27 +117,19 @@
- path: results/mpileup
should_exist: false
- path: results/reports/mosdepth/sample3/sample3.recal.global.dist.txt
- md5sum: d41d8cd98f00b204e9800998ecf8427e
- path: results/reports/mosdepth/sample3/sample3.recal.summary.txt
- md5sum: d41d8cd98f00b204e9800998ecf8427e
- path: results/reports/mosdepth/sample3/sample3.recal.per-base.bed.gz
- md5sum: 1a60c330fb42841e8dcf3cd507a70bfc
- path: results/reports/mosdepth/sample3/sample3.recal.per-base.bed.gz.csi
- md5sum: d41d8cd98f00b204e9800998ecf8427e
- path: results/reports/samtools/sample3/sample3.recal.cram.stats
# conda changes md5sums for test
- path: results/reports/mosdepth/sample4/sample4.recal.global.dist.txt
- md5sum: d41d8cd98f00b204e9800998ecf8427e
- path: results/reports/mosdepth/sample4/sample4.recal.summary.txt
- md5sum: d41d8cd98f00b204e9800998ecf8427e
- path: results/reports/mosdepth/sample4/sample4.recal.per-base.bed.gz
- md5sum: 1a60c330fb42841e8dcf3cd507a70bfc
- path: results/reports/mosdepth/sample4/sample4.recal.per-base.bed.gz.csi
- md5sum: d41d8cd98f00b204e9800998ecf8427e
- path: results/reports/samtools/sample4/sample4.recal.cram.stats
# conda changes md5sums for test
- name: Run variant calling on tumor_only sample with controlfreec
- command: nextflow run main.nf -profile test_cache,tools_tumoronly --tools controlfreec -stub-run --outdir results
+ command: nextflow run main.nf -profile test,tools_tumoronly --tools controlfreec -stub-run --outdir results
tags:
- controlfreec
- tumor_only
@@ -190,13 +172,8 @@
- path: results/mpileup
should_exist: false
- path: results/reports/mosdepth/sample2/sample2.recal.global.dist.txt
- md5sum: d41d8cd98f00b204e9800998ecf8427e
- path: results/reports/mosdepth/sample2/sample2.recal.region.dist.txt
- md5sum: d41d8cd98f00b204e9800998ecf8427e
- path: results/reports/mosdepth/sample2/sample2.recal.summary.txt
- md5sum: d41d8cd98f00b204e9800998ecf8427e
- path: results/reports/mosdepth/sample2/sample2.recal.regions.bed.gz
- md5sum: 1a60c330fb42841e8dcf3cd507a70bfc
- path: results/reports/mosdepth/sample2/sample2.recal.regions.bed.gz.csi
- md5sum: d41d8cd98f00b204e9800998ecf8427e
- path: results/reports/samtools/sample2/sample2.recal.cram.stats
diff --git a/tests/test_deepvariant.yml b/tests/test_deepvariant.yml
index cead54aa47..d66f2e1aef 100644
--- a/tests/test_deepvariant.yml
+++ b/tests/test_deepvariant.yml
@@ -1,5 +1,5 @@
- name: Run variant calling on germline sample with deepvariant
- command: nextflow run main.nf -profile test_cache,tools_germline --tools deepvariant --outdir results
+ command: nextflow run main.nf -profile test,tools_germline --tools deepvariant --outdir results
tags:
- deepvariant
- germline
@@ -25,18 +25,13 @@
- path: results/deepvariant
should_exist: false
- path: results/reports/mosdepth/sample1/sample1.recal.mosdepth.global.dist.txt
- md5sum: 69e29702ef01fd8f6c7a5468fc35a16a
- path: results/reports/mosdepth/sample1/sample1.recal.mosdepth.region.dist.txt
- md5sum: 6ec49cd7d510c2eb3d9d90fdb79b783a
- path: results/reports/mosdepth/sample1/sample1.recal.mosdepth.summary.txt
- md5sum: 103098d0bf76ed82d2b87d5f242b099a
- path: results/reports/mosdepth/sample1/sample1.recal.regions.bed.gz
- md5sum: b5888cf7395c57d39879a5faa6159eb3
- path: results/reports/mosdepth/sample1/sample1.recal.regions.bed.gz.csi
- md5sum: 9cb0ad7039a3b703d16ca7d5b835c0ee
- path: results/reports/samtools/sample1/sample1.recal.cram.stats
- name: Run variant calling on germline sample with deepvariant without intervals
- command: nextflow run main.nf -profile test_cache,tools_germline --tools deepvariant --no_intervals --outdir results
+ command: nextflow run main.nf -profile test,tools_germline --tools deepvariant --no_intervals --outdir results
tags:
- deepvariant
- germline
@@ -69,11 +64,7 @@
- path: results/deepvariant
should_exist: false
- path: results/reports/mosdepth/sample1/sample1.recal.mosdepth.global.dist.txt
- md5sum: 69e29702ef01fd8f6c7a5468fc35a16a
- path: results/reports/mosdepth/sample1/sample1.recal.mosdepth.summary.txt
- md5sum: d2775eb102acc5950f7f53883dcb503d
- path: results/reports/mosdepth/sample1/sample1.recal.per-base.bed.gz
- md5sum: 54431f155c9538809e8caf99d1a75ec7
- path: results/reports/mosdepth/sample1/sample1.recal.per-base.bed.gz.csi
- md5sum: c67dcd711b096eb42f43784d5eadbc0d
- path: results/reports/samtools/sample1/sample1.recal.cram.stats
diff --git a/tests/test_default.yml b/tests/test_default.yml
index 5368cfd9b0..97ebb3918d 100644
--- a/tests/test_default.yml
+++ b/tests/test_default.yml
@@ -30,25 +30,15 @@
- path: results/reports/markduplicates/test/test.md.cram.metrics
contains: ["test 17094 1534 168 1046782 12429 197 0 0.635998", "1.0 0.999991 1171"]
- path: results/reports/mosdepth/test/test.md.mosdepth.global.dist.txt
- md5sum: b61e1acee11a6ddf7ce3232a5948a6a0
- path: results/reports/mosdepth/test/test.md.mosdepth.region.dist.txt
- md5sum: 1a382f98d488d2ae3df83a0d87caafc1
- path: results/reports/mosdepth/test/test.md.mosdepth.summary.txt
- md5sum: 839108358878ada89e1eaddf6e0541ba
- path: results/reports/mosdepth/test/test.md.regions.bed.gz
- md5sum: 0aaee6da65050bedcd40b9fbf0622873
- path: results/reports/mosdepth/test/test.md.regions.bed.gz.csi
- md5sum: 544e02fcca548749a0af758d0a2df352
- path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt
- md5sum: b61e1acee11a6ddf7ce3232a5948a6a0
- path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt
- md5sum: 1a382f98d488d2ae3df83a0d87caafc1
- path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt
- md5sum: 839108358878ada89e1eaddf6e0541ba
- path: results/reports/mosdepth/test/test.recal.regions.bed.gz
- md5sum: 0aaee6da65050bedcd40b9fbf0622873
- path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi
- md5sum: 544e02fcca548749a0af758d0a2df352
- path: results/reports/samtools/test/test.md.cram.stats
# conda changes md5sums for test
- path: results/reports/samtools/test/test.recal.cram.stats
diff --git a/tests/test_fastp.yml b/tests/test_fastp.yml
index 7ea4dc4bd7..20eab4065f 100644
--- a/tests/test_fastp.yml
+++ b/tests/test_fastp.yml
@@ -1,5 +1,5 @@
- name: Run trimming pipeline
- command: nextflow run main.nf -profile test_cache,trimming --save_trimmed --outdir results
+ command: nextflow run main.nf -profile test,trimming --save_trimmed --outdir results
tags:
- fastp
- preprocessing
@@ -31,31 +31,21 @@
- path: results/reports/markduplicates/test/test.md.cram.metrics
contains: ["test 16608 1860 160 1046616 12117 256 0 0.621261"]
- path: results/reports/mosdepth/test/test.md.mosdepth.global.dist.txt
- md5sum: 3098d33090a0f90f6fc16d497d2ce644
- path: results/reports/mosdepth/test/test.md.mosdepth.region.dist.txt
- md5sum: 057a02943301a5acec55d19a5a629f11
- path: results/reports/mosdepth/test/test.md.mosdepth.summary.txt
- md5sum: fef22f026f7b4a89ab60c715689c5591
- path: results/reports/mosdepth/test/test.md.regions.bed.gz
- md5sum: cca0f725bea04688b39f2ea8ad2e1605
- path: results/reports/mosdepth/test/test.md.regions.bed.gz.csi
- md5sum: a5ad8f917979f62eacfff1461529dbaa
- path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt
- md5sum: 3098d33090a0f90f6fc16d497d2ce644
- path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt
- md5sum: 057a02943301a5acec55d19a5a629f11
- path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt
- md5sum: fef22f026f7b4a89ab60c715689c5591
- path: results/reports/mosdepth/test/test.recal.regions.bed.gz
- md5sum: cca0f725bea04688b39f2ea8ad2e1605
- path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi
- md5sum: a5ad8f917979f62eacfff1461529dbaa
- path: results/reports/samtools/test/test.md.cram.stats
# conda changes md5sums for test
- path: results/reports/samtools/test/test.recal.cram.stats
# conda changes md5sums for test
- name: Run split fastq module
- command: nextflow run main.nf -profile test_cache,split_fastq --outdir results
+ command: nextflow run main.nf -profile test,split_fastq --outdir results
tags:
- fastp
- preprocessing
@@ -90,25 +80,15 @@
- path: results/reports/markduplicates/test/test.md.cram.metrics
contains: ["test 17482 890 170 1047682 12552 69 0 0.65881"]
- path: results/reports/mosdepth/test/test.md.mosdepth.global.dist.txt
- md5sum: 3626e543b91aa564f0056747827366d3
- path: results/reports/mosdepth/test/test.md.mosdepth.region.dist.txt
- md5sum: e3442f1098899a22748d07ef436925f6
- path: results/reports/mosdepth/test/test.md.mosdepth.summary.txt
- md5sum: 2873e7f9c9aede39942731894a6077d1
- path: results/reports/mosdepth/test/test.md.regions.bed.gz
- md5sum: 948108074663677f9225fd0574658ca1
- path: results/reports/mosdepth/test/test.md.regions.bed.gz.csi
- md5sum: d5f1c9389ecf52ba839e834780a94549
- path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt
- md5sum: 3626e543b91aa564f0056747827366d3
- path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt
- md5sum: e3442f1098899a22748d07ef436925f6
- path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt
- md5sum: 2873e7f9c9aede39942731894a6077d1
- path: results/reports/mosdepth/test/test.recal.regions.bed.gz
- md5sum: 948108074663677f9225fd0574658ca1
- path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi
- md5sum: d5f1c9389ecf52ba839e834780a94549
- path: results/reports/samtools/test/test.md.cram.stats
# conda changes md5sums for test
- path: results/reports/samtools/test/test.recal.cram.stats
diff --git a/tests/test_freebayes.yml b/tests/test_freebayes.yml
index bd76fa1411..d4d85f0a1f 100644
--- a/tests/test_freebayes.yml
+++ b/tests/test_freebayes.yml
@@ -1,5 +1,5 @@
- name: Run variant calling on germline sample with freebayes
- command: nextflow run main.nf -profile test_cache,targeted --tools freebayes --outdir results
+ command: nextflow run main.nf -profile test,targeted --tools freebayes --outdir results
tags:
- freebayes
- germline
@@ -30,33 +30,19 @@
- path: results/reports/markduplicates/test/test.md.cram.metrics
contains: ["test 17094 1534 168 1046782 12429 197 0 0.635998", "1.0 0.999991 1171"]
- path: results/reports/mosdepth/test/test.md.mosdepth.global.dist.txt
- md5sum: e4ce28ba1c331dc08bc53a0189908f77
- path: results/reports/mosdepth/test/test.md.mosdepth.region.dist.txt
- md5sum: 04d9f20dc5306990eec982a3c5a7d107
- path: results/reports/mosdepth/test/test.md.mosdepth.summary.txt
- md5sum: 70b4bbe29bd5e7c4ea39b6caf3316096
- path: results/reports/mosdepth/test/test.md.per-base.bed.gz
- md5sum: 2a0c38fb19d6a1f81ca2018e59e7bfcf
- path: results/reports/mosdepth/test/test.md.per-base.bed.gz.csi
- md5sum: 0714f8c677277168b9f95d3a43ea5237
- path: results/reports/mosdepth/test/test.md.regions.bed.gz
- md5sum: eb0bc92c253326a109e73af98c9a7d4b
- path: results/reports/mosdepth/test/test.md.regions.bed.gz.csi
- md5sum: c6d1ac97ef4dfe43731c8368d8391cab
- path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt
- md5sum: 9c1d90e0fed14b710098b7724b602aea
- path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt
- md5sum: 04d9f20dc5306990eec982a3c5a7d107
- path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt
- md5sum: 17dfb78b147488eb8fd450294de4a35e
- path: results/reports/mosdepth/test/test.recal.per-base.bed.gz
- md5sum: fb6804911f9d437d0251869fe112a528
- path: results/reports/mosdepth/test/test.recal.per-base.bed.gz.csi
- md5sum: 033032cdbb3a2b74dd41dac89628112c
- path: results/reports/mosdepth/test/test.recal.regions.bed.gz
- md5sum: eb0bc92c253326a109e73af98c9a7d4b
- path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi
- md5sum: c6d1ac97ef4dfe43731c8368d8391cab
- path: results/reports/samtools/test/test.md.cram.stats
# conda changes md5sums for test
- path: results/reports/samtools/test/test.recal.cram.stats
@@ -73,7 +59,7 @@
- path: results/freebayes
should_exist: false
- name: Run variant calling on germline sample with freebayes without intervals
- command: nextflow run main.nf -profile test_cache --tools freebayes --no_intervals --outdir results
+ command: nextflow run main.nf -profile test --tools freebayes --no_intervals --outdir results
tags:
- freebayes
- germline
@@ -111,25 +97,15 @@
- path: results/reports/markduplicates/test/test.md.cram.metrics
contains: ["test 17094 1534 168 1046782 12429 197 0 0.635998", "1.0 0.999991 1171"]
- path: results/reports/mosdepth/test/test.md.mosdepth.global.dist.txt
- md5sum: b61e1acee11a6ddf7ce3232a5948a6a0
- path: results/reports/mosdepth/test/test.md.mosdepth.region.dist.txt
- md5sum: 1a382f98d488d2ae3df83a0d87caafc1
- path: results/reports/mosdepth/test/test.md.mosdepth.summary.txt
- md5sum: 839108358878ada89e1eaddf6e0541ba
- path: results/reports/mosdepth/test/test.md.regions.bed.gz
- md5sum: 0aaee6da65050bedcd40b9fbf0622873
- path: results/reports/mosdepth/test/test.md.regions.bed.gz.csi
- md5sum: 544e02fcca548749a0af758d0a2df352
- path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt
- md5sum: b61e1acee11a6ddf7ce3232a5948a6a0
- path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt
- md5sum: 1a382f98d488d2ae3df83a0d87caafc1
- path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt
- md5sum: 839108358878ada89e1eaddf6e0541ba
- path: results/reports/mosdepth/test/test.recal.regions.bed.gz
- md5sum: 0aaee6da65050bedcd40b9fbf0622873
- path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi
- md5sum: 544e02fcca548749a0af758d0a2df352
- path: results/reports/samtools/test/test.md.cram.stats
# conda changes md5sums for test
- path: results/reports/samtools/test/test.recal.cram.stats
@@ -146,7 +122,7 @@
- path: results/freebayes
should_exist: false
- name: Run variant calling on somatic sample with freebayes
- command: nextflow run main.nf -profile test_cache,pair,targeted --tools freebayes --outdir results
+ command: nextflow run main.nf -profile test,pair,targeted --tools freebayes --outdir results
tags:
- freebayes
- somatic
@@ -191,61 +167,33 @@
- path: results/reports/markduplicates/test2/test2.md.cram.metrics
contains: ["test2 10103 880 35 523579 4837 2 0 0.408076 193306", "1.0 1 876 876", "100.0 80.515303 0 0"]
- path: results/reports/mosdepth/test/test.md.mosdepth.global.dist.txt
- md5sum: 5a0679057c530e5945c9c5a3a17312dc
- path: results/reports/mosdepth/test/test.md.mosdepth.region.dist.txt
- md5sum: 835fdc6fa52cc33e6fb76c0c20a8a6c3
- path: results/reports/mosdepth/test/test.md.mosdepth.summary.txt
- md5sum: dcc9ab2bf3248903e02d8da87e678977
- path: results/reports/mosdepth/test/test.md.per-base.bed.gz
- md5sum: 5724f1c6b6a0e63e25ec8a0f38edfda6
- path: results/reports/mosdepth/test/test.md.per-base.bed.gz.csi
- md5sum: b0ab630c3241fbd7581b7a38d944ff8b
- path: results/reports/mosdepth/test/test.md.regions.bed.gz
- md5sum: 91e0d531f1bab64711ecefe52bfc8255
- path: results/reports/mosdepth/test/test.md.regions.bed.gz.csi
- md5sum: c6d1ac97ef4dfe43731c8368d8391cab
- path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt
- md5sum: 0b3162def977123809598639f7698121
- path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt
- md5sum: 835fdc6fa52cc33e6fb76c0c20a8a6c3
- path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt
- md5sum: a8455eb2947de529abfa62b303986e0f
- path: results/reports/mosdepth/test/test.recal.per-base.bed.gz
- md5sum: d9fa560ff78ae106cfee9db2c90801b5
- path: results/reports/mosdepth/test/test.recal.per-base.bed.gz.csi
- md5sum: 4816eeb9af254ca40177b08cf11b98d2
- path: results/reports/mosdepth/test/test.recal.regions.bed.gz
- md5sum: 91e0d531f1bab64711ecefe52bfc8255
- path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi
- md5sum: c6d1ac97ef4dfe43731c8368d8391cab
- path: results/reports/mosdepth/test2/test2.md.mosdepth.global.dist.txt
- md5sum: f25166c3a0051bb4d8c11a210278de6c
- path: results/reports/mosdepth/test2/test2.md.mosdepth.region.dist.txt
- md5sum: 3211135329e4077bd9bf0ba488e14371
- path: results/reports/mosdepth/test2/test2.md.mosdepth.summary.txt
- md5sum: ce0eb6d33c6d0dc720fbc6d1811abef8
- path: results/reports/mosdepth/test2/test2.md.per-base.bed.gz
- md5sum: 55c160e8f3c8c7761524646426611f6b
- path: results/reports/mosdepth/test2/test2.md.per-base.bed.gz.csi
- md5sum: 4205a09ede17cdbdaad45e3553f73105
- path: results/reports/mosdepth/test2/test2.md.regions.bed.gz
- md5sum: 1dd426a45f967a9f37dcddcaea29a582
- path: results/reports/mosdepth/test2/test2.md.regions.bed.gz.csi
- md5sum: c6d1ac97ef4dfe43731c8368d8391cab
- path: results/reports/mosdepth/test2/test2.recal.mosdepth.global.dist.txt
- md5sum: a1ef7e662ce993da4668e804952014ce
- path: results/reports/mosdepth/test2/test2.recal.mosdepth.region.dist.txt
- md5sum: 3211135329e4077bd9bf0ba488e14371
- path: results/reports/mosdepth/test2/test2.recal.mosdepth.summary.txt
- md5sum: 70ad653c0c98baeeaf5085f1209a7bdb
- path: results/reports/mosdepth/test2/test2.recal.per-base.bed.gz
- md5sum: 250a9f15a7d3f102435fa98adccf48a3
- path: results/reports/mosdepth/test2/test2.recal.per-base.bed.gz.csi
- md5sum: 8072f447199c60f24b01eede8b557333
- path: results/reports/mosdepth/test2/test2.recal.regions.bed.gz
- md5sum: 1dd426a45f967a9f37dcddcaea29a582
- path: results/reports/mosdepth/test2/test2.recal.regions.bed.gz.csi
- md5sum: c6d1ac97ef4dfe43731c8368d8391cab
- path: results/reports/samtools/test/test.md.cram.stats
# conda changes md5sums for test
- path: results/reports/samtools/test/test.recal.cram.stats
@@ -276,7 +224,7 @@
- path: results/freebayes
should_exist: false
- name: Run variant calling on somatic sample with freebayes without intervals
- command: nextflow run main.nf -profile test_cache,pair,targeted --tools freebayes --no_intervals --outdir results
+ command: nextflow run main.nf -profile test,pair,targeted --tools freebayes --no_intervals --outdir results
tags:
- freebayes
- somatic
@@ -328,37 +276,21 @@
- path: results/reports/markduplicates/test2/test2.md.cram.metrics
contains: ["test2 10103 880 35 523579 4837 2 0 0.408076 193306", "1.0 1 876 876", "100.0 80.515303 0 0"]
- path: results/reports/mosdepth/test/test.md.mosdepth.global.dist.txt
- md5sum: 5a0679057c530e5945c9c5a3a17312dc
- path: results/reports/mosdepth/test/test.md.mosdepth.summary.txt
- md5sum: 0010c2396a3173c7cf4983abe2eb6a4c
- path: results/reports/mosdepth/test/test.md.per-base.bed.gz
- md5sum: 5724f1c6b6a0e63e25ec8a0f38edfda6
- path: results/reports/mosdepth/test/test.md.per-base.bed.gz.csi
- md5sum: b0ab630c3241fbd7581b7a38d944ff8b
- path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt
- md5sum: 5a0679057c530e5945c9c5a3a17312dc
- path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt
- md5sum: 0010c2396a3173c7cf4983abe2eb6a4c
- path: results/reports/mosdepth/test/test.recal.per-base.bed.gz
- md5sum: 5724f1c6b6a0e63e25ec8a0f38edfda6
- path: results/reports/mosdepth/test/test.recal.per-base.bed.gz.csi
- md5sum: b0ab630c3241fbd7581b7a38d944ff8b
- path: results/reports/mosdepth/test2/test2.md.mosdepth.global.dist.txt
- md5sum: f25166c3a0051bb4d8c11a210278de6c
- path: results/reports/mosdepth/test2/test2.md.mosdepth.summary.txt
- md5sum: d5e4084de2ea2a0a7b60b2d71c804d4b
- path: results/reports/mosdepth/test2/test2.md.per-base.bed.gz
- md5sum: 55c160e8f3c8c7761524646426611f6b
- path: results/reports/mosdepth/test2/test2.md.per-base.bed.gz.csi
- md5sum: 4205a09ede17cdbdaad45e3553f73105
- path: results/reports/mosdepth/test2/test2.recal.mosdepth.global.dist.txt
- md5sum: f25166c3a0051bb4d8c11a210278de6c
- path: results/reports/mosdepth/test2/test2.recal.mosdepth.summary.txt
- md5sum: d5e4084de2ea2a0a7b60b2d71c804d4b
- path: results/reports/mosdepth/test2/test2.recal.per-base.bed.gz
- md5sum: 55c160e8f3c8c7761524646426611f6b
- path: results/reports/mosdepth/test2/test2.recal.per-base.bed.gz.csi
- md5sum: 4205a09ede17cdbdaad45e3553f73105
- path: results/reports/samtools/test/test.md.cram.stats
# conda changes md5sums for test
- path: results/reports/samtools/test/test.recal.cram.stats
@@ -389,7 +321,7 @@
- path: results/freebayes
should_exist: false
- name: Run variant calling on tumor_only sample with freebayes
- command: nextflow run main.nf -profile test_cache,tools_tumoronly --tools freebayes --outdir results
+ command: nextflow run main.nf -profile test,tools_tumoronly --tools freebayes --outdir results
tags:
- freebayes
- tumor_only
@@ -413,7 +345,7 @@
- path: results/freebayes
should_exist: false
- name: Run variant calling on tumor_only sample with freebayes without intervals
- command: nextflow run main.nf -profile test_cache,tools_tumoronly --tools freebayes --no_intervals --outdir results
+ command: nextflow run main.nf -profile test,tools_tumoronly --tools freebayes --no_intervals --outdir results
tags:
- freebayes
- no_intervals
diff --git a/tests/test_gatk4spark.yml b/tests/test_gatk4spark.yml
index 6462bd130a..cdb2cf3292 100644
--- a/tests/test_gatk4spark.yml
+++ b/tests/test_gatk4spark.yml
@@ -1,5 +1,5 @@
- name: Run default pipeline with gatk4spark
- command: nextflow run main.nf -profile test_cache,use_gatk_spark,spark --outdir results
+ command: nextflow run main.nf -profile test,use_gatk_spark,spark --outdir results
tags:
- gatk4spark
- preprocessing
@@ -25,23 +25,14 @@
- path: results/reports/markduplicates/test2/test2.md.cram.metrics
# text-based file changes md5sums on reruns
- path: results/reports/mosdepth/test2/test2.md.mosdepth.global.dist.txt
- md5sum: 85d38a74ce189b9110c57cd94bc26757
- path: results/reports/mosdepth/test2/test2.md.mosdepth.region.dist.txt
- md5sum: 286d57b7d9b3a95ef18ab2eb7f913d81
- path: results/reports/mosdepth/test2/test2.md.mosdepth.summary.txt
- md5sum: 04b69ef7f00199dcea7822a79d2c7bd7
- path: results/reports/mosdepth/test2/test2.md.regions.bed.gz
- md5sum: 4e6c360aea7f05d801b2ea5685fe154a
- path: results/reports/mosdepth/test2/test2.md.regions.bed.gz.csi
- md5sum: 5bf5fc178e4faf2462427502c3666004
- path: results/reports/mosdepth/test2/test2.recal.mosdepth.global.dist.txt
- md5sum: 85d38a74ce189b9110c57cd94bc26757
- path: results/reports/mosdepth/test2/test2.recal.mosdepth.region.dist.txt
- md5sum: 286d57b7d9b3a95ef18ab2eb7f913d81
- path: results/reports/mosdepth/test2/test2.recal.mosdepth.summary.txt
- md5sum: 04b69ef7f00199dcea7822a79d2c7bd7
- path: results/reports/mosdepth/test2/test2.recal.regions.bed.gz
- md5sum: 4e6c360aea7f05d801b2ea5685fe154a
- path: results/reports/samtools/test2/test2.md.cram.stats
# conda changes md5sums for test
- path: results/reports/samtools/test2/test2.recal.cram.stats
@@ -49,7 +40,7 @@
- path: results/preprocessing/mapped/
should_exist: false
- name: Run default pipeline with gatk4spark and skipping all QC steps
- command: nextflow run main.nf -profile test_cache,use_gatk_spark,spark --skip_tools fastqc,markduplicates_report,mosdepth,multiqc,samtools --outdir results
+ command: nextflow run main.nf -profile test,use_gatk_spark,spark --skip_tools fastqc,markduplicates_report,mosdepth,multiqc,samtools --outdir results
tags:
- gatk4spark
- preprocessing
@@ -82,7 +73,7 @@
- path: results/reports/samtools
should_exist: false
- name: Run save_output_as_bam with gatk4 spark
- command: nextflow run main.nf -profile test_cache,use_gatk_spark,spark --save_output_as_bam --outdir results
+ command: nextflow run main.nf -profile test,use_gatk_spark,spark --save_output_as_bam --outdir results
tags:
- gatk4spark
- preprocessing
@@ -109,25 +100,15 @@
- path: results/reports/markduplicates/test2/test2.md.cram.metrics
# text-based file changes md5sums on reruns
- path: results/reports/mosdepth/test2/test2.md.mosdepth.global.dist.txt
- md5sum: 85d38a74ce189b9110c57cd94bc26757
- path: results/reports/mosdepth/test2/test2.md.mosdepth.region.dist.txt
- md5sum: 286d57b7d9b3a95ef18ab2eb7f913d81
- path: results/reports/mosdepth/test2/test2.md.mosdepth.summary.txt
- md5sum: 04b69ef7f00199dcea7822a79d2c7bd7
- path: results/reports/mosdepth/test2/test2.md.regions.bed.gz
- md5sum: 4e6c360aea7f05d801b2ea5685fe154a
- path: results/reports/mosdepth/test2/test2.md.regions.bed.gz.csi
- md5sum: 5bf5fc178e4faf2462427502c3666004
- path: results/reports/mosdepth/test2/test2.recal.mosdepth.global.dist.txt
- md5sum: 85d38a74ce189b9110c57cd94bc26757
- path: results/reports/mosdepth/test2/test2.recal.mosdepth.region.dist.txt
- md5sum: 286d57b7d9b3a95ef18ab2eb7f913d81
- path: results/reports/mosdepth/test2/test2.recal.mosdepth.summary.txt
- md5sum: 04b69ef7f00199dcea7822a79d2c7bd7
- path: results/reports/mosdepth/test2/test2.recal.regions.bed.gz
- md5sum: 4e6c360aea7f05d801b2ea5685fe154a
- path: results/reports/mosdepth/test2/test2.recal.regions.bed.gz.csi
- md5sum: 5bf5fc178e4faf2462427502c3666004
- path: results/reports/samtools/test2/test2.md.cram.stats
# conda changes md5sums for test
- path: results/reports/samtools/test2/test2.recal.cram.stats
diff --git a/tests/test_haplotypecaller.yml b/tests/test_haplotypecaller.yml
index 2f76698774..7912e49909 100644
--- a/tests/test_haplotypecaller.yml
+++ b/tests/test_haplotypecaller.yml
@@ -1,5 +1,5 @@
- name: Run variant calling on germline sample with haplotypecaller
- command: nextflow run main.nf -profile test_cache,targeted --input ./tests/csv/3.0/mapped_single_bam.csv --tools haplotypecaller --step variant_calling --outdir results
+ command: nextflow run main.nf -profile test,targeted --input ./tests/csv/3.0/mapped_single_bam.csv --tools haplotypecaller --step variant_calling --outdir results
tags:
- germline
- haplotypecaller
@@ -35,19 +35,14 @@
- path: results/haplotypecaller
should_exist: false
- path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt
- md5sum: e82e90c7d508a135b5a8a7cd6933452e
- path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt
- md5sum: 3a2030e5e8af7bc12720c3a5592bf921
- path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt
- md5sum: 615c5c5019d88045a9ff5bbe6e63d270
- path: results/reports/mosdepth/test/test.recal.regions.bed.gz
- md5sum: 9f1ea20e7461db948ba21f70c4d1b3ba
- path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi
- md5sum: 5c00a1d457c387d6e71848a6d897e309
- path: results/reports/samtools/test/test.recal.cram.stats
- name: Run variant calling on germline sample with haplotypecaller without intervals
- command: nextflow run main.nf -profile test_cache,targeted --input ./tests/csv/3.0/mapped_single_bam.csv --tools haplotypecaller --step variant_calling --no_intervals --outdir results
+ command: nextflow run main.nf -profile test,targeted --input ./tests/csv/3.0/mapped_single_bam.csv --tools haplotypecaller --step variant_calling --no_intervals --outdir results
tags:
- germline
- haplotypecaller
@@ -90,11 +85,7 @@
- path: results/haplotypecaller
should_exist: false
- path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt
- md5sum: e82e90c7d508a135b5a8a7cd6933452e
- path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt
- md5sum: 4f0d231060cbde4efdd673863bd2fb59
- path: results/reports/mosdepth/test/test.recal.per-base.bed.gz
- md5sum: bc1df47d46f818fee5275975925d769a
- path: results/reports/mosdepth/test/test.recal.per-base.bed.gz.csi
- md5sum: 9e649ac749ff6c6073bef5ab63e8aaa4
- path: results/reports/samtools/test/test.recal.cram.stats
diff --git a/tests/test_haplotypecaller_skip_filter.yml b/tests/test_haplotypecaller_skip_filter.yml
index 9b68f220e6..b96157f868 100644
--- a/tests/test_haplotypecaller_skip_filter.yml
+++ b/tests/test_haplotypecaller_skip_filter.yml
@@ -1,5 +1,5 @@
- name: Run variant calling on germline sample with haplotypecaller and skip filter
- command: nextflow run main.nf -profile test_cache,targeted --input ./tests/csv/3.0/mapped_single_bam.csv --tools haplotypecaller --step variant_calling --skip_tools haplotypecaller_filter --outdir results
+ command: nextflow run main.nf -profile test,targeted --input ./tests/csv/3.0/mapped_single_bam.csv --tools haplotypecaller --step variant_calling --skip_tools haplotypecaller_filter --outdir results
tags:
- germline
- haplotypecaller_skip_filter
@@ -39,18 +39,13 @@
- path: results/haplotypecaller
should_exist: false
- path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt
- md5sum: e82e90c7d508a135b5a8a7cd6933452e
- path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt
- md5sum: 3a2030e5e8af7bc12720c3a5592bf921
- path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt
- md5sum: 615c5c5019d88045a9ff5bbe6e63d270
- path: results/reports/mosdepth/test/test.recal.regions.bed.gz
- md5sum: 9f1ea20e7461db948ba21f70c4d1b3ba
- path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi
- md5sum: 5c00a1d457c387d6e71848a6d897e309
- path: results/reports/samtools/test/test.recal.cram.stats
- name: Run variant calling on germline sample with haplotypecaller without intervals and skip filter
- command: nextflow run main.nf -profile test_cache,targeted --input ./tests/csv/3.0/mapped_single_bam.csv --tools haplotypecaller --step variant_calling --skip_tools haplotypecaller_filter --no_intervals --outdir results
+ command: nextflow run main.nf -profile test,targeted --input ./tests/csv/3.0/mapped_single_bam.csv --tools haplotypecaller --step variant_calling --skip_tools haplotypecaller_filter --no_intervals --outdir results
tags:
- germline
- haplotypecaller_skip_filter
@@ -93,11 +88,7 @@
- path: results/haplotypecaller
should_exist: false
- path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt
- md5sum: e82e90c7d508a135b5a8a7cd6933452e
- path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt
- md5sum: 4f0d231060cbde4efdd673863bd2fb59
- path: results/reports/mosdepth/test/test.recal.per-base.bed.gz
- md5sum: bc1df47d46f818fee5275975925d769a
- path: results/reports/mosdepth/test/test.recal.per-base.bed.gz.csi
- md5sum: 9e649ac749ff6c6073bef5ab63e8aaa4
- path: results/reports/samtools/test/test.recal.cram.stats
diff --git a/tests/test_intervals.yml b/tests/test_intervals.yml
index 0196376807..21326859d3 100644
--- a/tests/test_intervals.yml
+++ b/tests/test_intervals.yml
@@ -1,5 +1,5 @@
- name: Run default pipeline with target bed
- command: nextflow run main.nf -profile test_cache,targeted --outdir results
+ command: nextflow run main.nf -profile test,targeted --outdir results
tags:
- intervals
- preprocessing
@@ -26,39 +26,25 @@
- path: results/reports/markduplicates/test/test.md.cram.metrics
contains: ["test 17094 1534 168 1046782 12429 197 0 0.635998", "1.0 0.999991 1171"]
- path: results/reports/mosdepth/test/test.md.mosdepth.global.dist.txt
- md5sum: e4ce28ba1c331dc08bc53a0189908f77
- path: results/reports/mosdepth/test/test.md.mosdepth.region.dist.txt
- md5sum: 04d9f20dc5306990eec982a3c5a7d107
- path: results/reports/mosdepth/test/test.md.mosdepth.summary.txt
- md5sum: 70b4bbe29bd5e7c4ea39b6caf3316096
- path: results/reports/mosdepth/test/test.md.per-base.bed.gz
- md5sum: 2a0c38fb19d6a1f81ca2018e59e7bfcf
- path: results/reports/mosdepth/test/test.md.per-base.bed.gz.csi
- md5sum: 0714f8c677277168b9f95d3a43ea5237
- path: results/reports/mosdepth/test/test.md.regions.bed.gz
- md5sum: eb0bc92c253326a109e73af98c9a7d4b
- path: results/reports/mosdepth/test/test.md.regions.bed.gz.csi
- md5sum: c6d1ac97ef4dfe43731c8368d8391cab
- path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt
- md5sum: 9c1d90e0fed14b710098b7724b602aea
- path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt
- md5sum: 04d9f20dc5306990eec982a3c5a7d107
- path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt
- md5sum: 17dfb78b147488eb8fd450294de4a35e
- path: results/reports/mosdepth/test/test.recal.per-base.bed.gz
- md5sum: fb6804911f9d437d0251869fe112a528
- path: results/reports/mosdepth/test/test.recal.per-base.bed.gz.csi
- md5sum: 033032cdbb3a2b74dd41dac89628112c
- path: results/reports/mosdepth/test/test.recal.regions.bed.gz
- md5sum: eb0bc92c253326a109e73af98c9a7d4b
- path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi
- md5sum: c6d1ac97ef4dfe43731c8368d8391cab
- path: results/reports/samtools/test/test.md.cram.stats
# conda changes md5sums for test
- path: results/reports/samtools/test/test.recal.cram.stats
# conda changes md5sums for test
- name: Run pipeline with intervals false
- command: nextflow run main.nf -profile test_cache --intervals false --save_reference --outdir results
+ command: nextflow run main.nf -profile test --intervals false --save_reference --outdir results
tags:
- intervals
- intervals_false
@@ -89,27 +75,19 @@
- path: results/reports/markduplicates/test/test.md.cram.metrics
contains: ["test 17094 1534 168 1046782 12429 197 0 0.635998", "1.0 0.999991 1171"]
- path: results/reports/mosdepth/test/test.md.mosdepth.global.dist.txt
- md5sum: b61e1acee11a6ddf7ce3232a5948a6a0
- path: results/reports/mosdepth/test/test.md.mosdepth.region.dist.txt
- md5sum: 1a382f98d488d2ae3df83a0d87caafc1
- path: results/reports/mosdepth/test/test.md.mosdepth.summary.txt
- md5sum: 839108358878ada89e1eaddf6e0541ba
- path: results/reports/mosdepth/test/test.md.regions.bed.gz
- md5sum: 0aaee6da65050bedcd40b9fbf0622873
- path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt
- md5sum: b61e1acee11a6ddf7ce3232a5948a6a0
- path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt
- md5sum: 1a382f98d488d2ae3df83a0d87caafc1
- path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt
- md5sum: 839108358878ada89e1eaddf6e0541ba
- path: results/reports/mosdepth/test/test.recal.regions.bed.gz
- md5sum: 0aaee6da65050bedcd40b9fbf0622873
- path: results/reports/samtools/test/test.md.cram.stats
# conda changes md5sums for test
- path: results/reports/samtools/test/test.recal.cram.stats
# conda changes md5sums for test
- name: Run default pipeline without intervals
- command: nextflow run main.nf -profile test_cache,no_intervals --outdir results
+ command: nextflow run main.nf -profile test,no_intervals --outdir results
tags:
- intervals
- no_intervals
@@ -142,25 +120,15 @@
- path: results/reports/markduplicates/test/test.md.cram.metrics
contains: ["test 17094 1534 168 1046782 12429 197 0 0.635998", "1.0 0.999991 1171"]
- path: results/reports/mosdepth/test/test.md.mosdepth.global.dist.txt
- md5sum: b61e1acee11a6ddf7ce3232a5948a6a0
- path: results/reports/mosdepth/test/test.md.mosdepth.region.dist.txt
- md5sum: 1a382f98d488d2ae3df83a0d87caafc1
- path: results/reports/mosdepth/test/test.md.mosdepth.summary.txt
- md5sum: 839108358878ada89e1eaddf6e0541ba
- path: results/reports/mosdepth/test/test.md.regions.bed.gz
- md5sum: 0aaee6da65050bedcd40b9fbf0622873
- path: results/reports/mosdepth/test/test.md.regions.bed.gz.csi
- md5sum: 544e02fcca548749a0af758d0a2df352
- path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt
- md5sum: b61e1acee11a6ddf7ce3232a5948a6a0
- path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt
- md5sum: 1a382f98d488d2ae3df83a0d87caafc1
- path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt
- md5sum: 839108358878ada89e1eaddf6e0541ba
- path: results/reports/mosdepth/test/test.recal.regions.bed.gz
- md5sum: 0aaee6da65050bedcd40b9fbf0622873
- path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi
- md5sum: 544e02fcca548749a0af758d0a2df352
- path: results/reports/samtools/test/test.md.cram.stats
# conda changes md5sums for test
- path: results/reports/samtools/test/test.recal.cram.stats
diff --git a/tests/test_joint_germline.yml b/tests/test_joint_germline.yml
index e01a7ea1a3..badaf3c807 100644
--- a/tests/test_joint_germline.yml
+++ b/tests/test_joint_germline.yml
@@ -1,5 +1,5 @@
- name: Run joint germline variant calling with haplotypecaller
- command: nextflow run main.nf -profile test_cache,targeted --input ./tests/csv/3.0/mapped_joint_bam.csv --tools haplotypecaller --step variant_calling --joint_germline --outdir results --known_snps_vqsr false --known_indels_vqsr false
+ command: nextflow run main.nf -profile test,targeted --input ./tests/csv/3.0/mapped_joint_bam.csv --tools haplotypecaller --step variant_calling --joint_germline --dbsnp_vqsr false --known_snps_vqsr false --known_indels_vqsr false --outdir results
tags:
- germline
- joint_germline
@@ -31,29 +31,19 @@
- path: results/haplotypecaller
should_exist: false
- path: results/reports/mosdepth/testN/testN.recal.mosdepth.global.dist.txt
- md5sum: e82e90c7d508a135b5a8a7cd6933452e
- path: results/reports/mosdepth/testN/testN.recal.mosdepth.region.dist.txt
- md5sum: 3a2030e5e8af7bc12720c3a5592bf921
- path: results/reports/mosdepth/testN/testN.recal.mosdepth.summary.txt
- md5sum: 615c5c5019d88045a9ff5bbe6e63d270
- path: results/reports/mosdepth/testN/testN.recal.regions.bed.gz
- md5sum: 9f1ea20e7461db948ba21f70c4d1b3ba
- path: results/reports/mosdepth/testN/testN.recal.regions.bed.gz.csi
- md5sum: 5c00a1d457c387d6e71848a6d897e309
- path: results/reports/samtools/testN/testN.recal.cram.stats
- path: results/reports/mosdepth/testT/testT.recal.mosdepth.global.dist.txt
- md5sum: ba97ed85645f77da6f3adad138b3cdb4
- path: results/reports/mosdepth/testT/testT.recal.mosdepth.region.dist.txt
- md5sum: a7eb835371dd0aaf347ccca7ebe1eb3b
- path: results/reports/mosdepth/testT/testT.recal.mosdepth.summary.txt
- md5sum: a937108cbf24c1430b79c861234ce22b
- path: results/reports/mosdepth/testT/testT.recal.regions.bed.gz
- md5sum: d2b579a74bf8d858f82869f073056252
- path: results/reports/mosdepth/testT/testT.recal.regions.bed.gz.csi
- md5sum: 5c00a1d457c387d6e71848a6d897e309
- path: results/reports/samtools/testT/testT.recal.cram.stats
- name: Run joint germline variant calling with haplotypecaller all intervals at once
- command: nextflow run main.nf -profile test_cache,targeted --input ./tests/csv/3.0/mapped_joint_bam.csv --tools haplotypecaller --step variant_calling --joint_germline --outdir results --nucleotides_per_second 100
+ command: nextflow run main.nf -profile test,targeted --input ./tests/csv/3.0/mapped_joint_bam.csv --tools haplotypecaller --step variant_calling --joint_germline --dbsnp_vqsr false --known_snps_vqsr false --known_indels_vqsr false --nucleotides_per_second 100 --outdir results
tags:
- germline
- joint_germline
@@ -85,29 +75,19 @@
- path: results/haplotypecaller
should_exist: false
- path: results/reports/mosdepth/testN/testN.recal.mosdepth.global.dist.txt
- md5sum: e82e90c7d508a135b5a8a7cd6933452e
- path: results/reports/mosdepth/testN/testN.recal.mosdepth.region.dist.txt
- md5sum: 3a2030e5e8af7bc12720c3a5592bf921
- path: results/reports/mosdepth/testN/testN.recal.mosdepth.summary.txt
- md5sum: 615c5c5019d88045a9ff5bbe6e63d270
- path: results/reports/mosdepth/testN/testN.recal.regions.bed.gz
- md5sum: 9f1ea20e7461db948ba21f70c4d1b3ba
- path: results/reports/mosdepth/testN/testN.recal.regions.bed.gz.csi
- md5sum: 5c00a1d457c387d6e71848a6d897e309
- path: results/reports/samtools/testN/testN.recal.cram.stats
- path: results/reports/mosdepth/testT/testT.recal.mosdepth.global.dist.txt
- md5sum: ba97ed85645f77da6f3adad138b3cdb4
- path: results/reports/mosdepth/testT/testT.recal.mosdepth.region.dist.txt
- md5sum: a7eb835371dd0aaf347ccca7ebe1eb3b
- path: results/reports/mosdepth/testT/testT.recal.mosdepth.summary.txt
- md5sum: a937108cbf24c1430b79c861234ce22b
- path: results/reports/mosdepth/testT/testT.recal.regions.bed.gz
- md5sum: d2b579a74bf8d858f82869f073056252
- path: results/reports/mosdepth/testT/testT.recal.regions.bed.gz.csi
- md5sum: 5c00a1d457c387d6e71848a6d897e309
- path: results/reports/samtools/testT/testT.recal.cram.stats
- name: Run joint germline variant calling with haplotypecaller with Stub for VQSR
- command: nextflow run main.nf -profile test_cache,tools_germline --input ./tests/csv/3.0/mapped_joint_bam.csv --tools haplotypecaller --step variant_calling --joint_germline --outdir results -stub-run
+ command: nextflow run main.nf -profile test,tools_germline --input ./tests/csv/3.0/mapped_joint_bam.csv --tools haplotypecaller --step variant_calling --joint_germline --outdir results -stub-run
tags:
- germline
- joint_germline
@@ -144,24 +124,14 @@
- path: results/haplotypecaller
should_exist: false
- path: results/reports/mosdepth/testN/testN.recal.global.dist.txt
- md5sum: d41d8cd98f00b204e9800998ecf8427e
- path: results/reports/mosdepth/testN/testN.recal.region.dist.txt
- md5sum: d41d8cd98f00b204e9800998ecf8427e
- path: results/reports/mosdepth/testN/testN.recal.summary.txt
- md5sum: d41d8cd98f00b204e9800998ecf8427e
- path: results/reports/mosdepth/testN/testN.recal.regions.bed.gz
- md5sum: 1a60c330fb42841e8dcf3cd507a70bfc
- path: results/reports/mosdepth/testN/testN.recal.regions.bed.gz.csi
- md5sum: d41d8cd98f00b204e9800998ecf8427e
- path: results/reports/samtools/testN/testN.recal.cram.stats
- path: results/reports/mosdepth/testT/testT.recal.global.dist.txt
- md5sum: d41d8cd98f00b204e9800998ecf8427e
- path: results/reports/mosdepth/testT/testT.recal.region.dist.txt
- md5sum: d41d8cd98f00b204e9800998ecf8427e
- path: results/reports/mosdepth/testT/testT.recal.summary.txt
- md5sum: d41d8cd98f00b204e9800998ecf8427e
- path: results/reports/mosdepth/testT/testT.recal.regions.bed.gz
- md5sum: 1a60c330fb42841e8dcf3cd507a70bfc
- path: results/reports/mosdepth/testT/testT.recal.regions.bed.gz.csi
- md5sum: d41d8cd98f00b204e9800998ecf8427e
- path: results/reports/samtools/testT/testT.recal.cram.stats
diff --git a/tests/test_manta.yml b/tests/test_manta.yml
index b119ca80b7..8b9dfbd168 100644
--- a/tests/test_manta.yml
+++ b/tests/test_manta.yml
@@ -1,5 +1,5 @@
- name: Run variant calling on germline sample with manta
- command: nextflow run main.nf -profile test_cache,tools_germline --tools manta --outdir results
+ command: nextflow run main.nf -profile test,tools_germline --tools manta --outdir results
tags:
- germline
- manta
@@ -23,18 +23,13 @@
- path: results/manta
should_exist: false
- path: results/reports/mosdepth/sample1/sample1.recal.mosdepth.global.dist.txt
- md5sum: 69e29702ef01fd8f6c7a5468fc35a16a
- path: results/reports/mosdepth/sample1/sample1.recal.mosdepth.region.dist.txt
- md5sum: 6ec49cd7d510c2eb3d9d90fdb79b783a
- path: results/reports/mosdepth/sample1/sample1.recal.mosdepth.summary.txt
- md5sum: 103098d0bf76ed82d2b87d5f242b099a
- path: results/reports/mosdepth/sample1/sample1.recal.regions.bed.gz
- md5sum: b5888cf7395c57d39879a5faa6159eb3
- path: results/reports/mosdepth/sample1/sample1.recal.regions.bed.gz.csi
- md5sum: 9cb0ad7039a3b703d16ca7d5b835c0ee
- path: results/reports/samtools/sample1/sample1.recal.cram.stats
- name: Run variant calling on germline sample with manta without intervals
- command: nextflow run main.nf -profile test_cache,tools_germline --tools manta --no_intervals --outdir results
+ command: nextflow run main.nf -profile test,tools_germline --tools manta --no_intervals --outdir results
tags:
- germline
- manta
@@ -65,16 +60,12 @@
- path: results/manta
should_exist: false
- path: results/reports/mosdepth/sample1/sample1.recal.mosdepth.global.dist.txt
- md5sum: 69e29702ef01fd8f6c7a5468fc35a16a
- path: results/reports/mosdepth/sample1/sample1.recal.mosdepth.summary.txt
- md5sum: d2775eb102acc5950f7f53883dcb503d
- path: results/reports/mosdepth/sample1/sample1.recal.per-base.bed.gz
- md5sum: 54431f155c9538809e8caf99d1a75ec7
- path: results/reports/mosdepth/sample1/sample1.recal.per-base.bed.gz.csi
- md5sum: c67dcd711b096eb42f43784d5eadbc0d
- path: results/reports/samtools/sample1/sample1.recal.cram.stats
- name: Run variant calling on tumor_only sample with manta
- command: nextflow run main.nf -profile test_cache,tools_tumoronly --tools manta --outdir results
+ command: nextflow run main.nf -profile test,tools_tumoronly --tools manta --outdir results
tags:
- manta
- tumor_only
@@ -98,18 +89,13 @@
- path: results/manta
should_exist: false
- path: results/reports/mosdepth/sample2/sample2.recal.mosdepth.global.dist.txt
- md5sum: f2dcd00a64947c49e8e4b93c2f4fbf27
- path: results/reports/mosdepth/sample2/sample2.recal.mosdepth.region.dist.txt
- md5sum: 39005ffaac22871ffaaf19656fe69c5b
- path: results/reports/mosdepth/sample2/sample2.recal.mosdepth.summary.txt
- md5sum: 68d4b98f17361fddf73052ead34fa370
- path: results/reports/mosdepth/sample2/sample2.recal.regions.bed.gz
- md5sum: 2819e995eafded35f53328c4ec19ba58
- path: results/reports/mosdepth/sample2/sample2.recal.regions.bed.gz.csi
- md5sum: 393c2749068304d8545b501b9d4658e4
- path: results/reports/samtools/sample2/sample2.recal.cram.stats
- name: Run variant calling on tumor_only sample with manta without intervals
- command: nextflow run main.nf -profile test_cache,tools_tumoronly --tools manta --no_intervals --outdir results
+ command: nextflow run main.nf -profile test,tools_tumoronly --tools manta --no_intervals --outdir results
tags:
- manta
- no_intervals
@@ -140,16 +126,12 @@
- path: results/manta
should_exist: false
- path: results/reports/mosdepth/sample2/sample2.recal.mosdepth.global.dist.txt
- md5sum: f2dcd00a64947c49e8e4b93c2f4fbf27
- path: results/reports/mosdepth/sample2/sample2.recal.mosdepth.summary.txt
- md5sum: 0a7300e56eda6fba7c7564f00aa000f0
- path: results/reports/mosdepth/sample2/sample2.recal.per-base.bed.gz
- md5sum: 3de4a9f4da2f2b4909ef192452a8d211
- path: results/reports/mosdepth/sample2/sample2.recal.per-base.bed.gz.csi
- md5sum: cfb07b0ba46e8468b4342edb243536f3
- path: results/reports/samtools/sample2/sample2.recal.cram.stats
- name: Run variant calling on somatic sample with manta
- command: nextflow run main.nf -profile test_cache,tools_somatic --tools manta --outdir results
+ command: nextflow run main.nf -profile test,tools_somatic --tools manta --outdir results
tags:
- manta
- somatic
@@ -197,31 +179,21 @@
- path: results/manta
should_exist: false
- path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.global.dist.txt
- md5sum: 69e29702ef01fd8f6c7a5468fc35a16a
- path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.region.dist.txt
- md5sum: 6ec49cd7d510c2eb3d9d90fdb79b783a
- path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.summary.txt
- md5sum: 103098d0bf76ed82d2b87d5f242b099a
- path: results/reports/mosdepth/sample3/sample3.recal.regions.bed.gz
- md5sum: b5888cf7395c57d39879a5faa6159eb3
- path: results/reports/mosdepth/sample3/sample3.recal.regions.bed.gz.csi
- md5sum: 9cb0ad7039a3b703d16ca7d5b835c0ee
- path: results/reports/samtools/sample3/sample3.recal.cram.stats
# conda changes md5sums for test
- path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.global.dist.txt
- md5sum: f2dcd00a64947c49e8e4b93c2f4fbf27
- path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.region.dist.txt
- md5sum: 39005ffaac22871ffaaf19656fe69c5b
- path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.summary.txt
- md5sum: 68d4b98f17361fddf73052ead34fa370
- path: results/reports/mosdepth/sample4/sample4.recal.regions.bed.gz
- md5sum: 2819e995eafded35f53328c4ec19ba58
- path: results/reports/mosdepth/sample4/sample4.recal.regions.bed.gz.csi
- md5sum: 393c2749068304d8545b501b9d4658e4
- path: results/reports/samtools/sample4/sample4.recal.cram.stats
# conda changes md5sums for test
- name: Run variant calling on somatic sample with manta without intervals
- command: nextflow run main.nf -profile test_cache,tools_somatic --tools manta --no_intervals --outdir results
+ command: nextflow run main.nf -profile test,tools_somatic --tools manta --no_intervals --outdir results
tags:
- manta
- no_intervals
@@ -276,22 +248,14 @@
- path: results/manta
should_exist: false
- path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.global.dist.txt
- md5sum: 69e29702ef01fd8f6c7a5468fc35a16a
- path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.summary.txt
- md5sum: d2775eb102acc5950f7f53883dcb503d
- path: results/reports/mosdepth/sample3/sample3.recal.per-base.bed.gz
- md5sum: 54431f155c9538809e8caf99d1a75ec7
- path: results/reports/mosdepth/sample3/sample3.recal.per-base.bed.gz.csi
- md5sum: c67dcd711b096eb42f43784d5eadbc0d
- path: results/reports/samtools/sample3/sample3.recal.cram.stats
# conda changes md5sums for test
- path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.global.dist.txt
- md5sum: f2dcd00a64947c49e8e4b93c2f4fbf27
- path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.summary.txt
- md5sum: 0a7300e56eda6fba7c7564f00aa000f0
- path: results/reports/mosdepth/sample4/sample4.recal.per-base.bed.gz
- md5sum: 3de4a9f4da2f2b4909ef192452a8d211
- path: results/reports/mosdepth/sample4/sample4.recal.per-base.bed.gz.csi
- md5sum: cfb07b0ba46e8468b4342edb243536f3
- path: results/reports/samtools/sample4/sample4.recal.cram.stats
# conda changes md5sums for test
diff --git a/tests/test_markduplicates_from_bam.yml b/tests/test_markduplicates_from_bam.yml
index d6191216bd..ab436a7ce2 100644
--- a/tests/test_markduplicates_from_bam.yml
+++ b/tests/test_markduplicates_from_bam.yml
@@ -1,5 +1,5 @@
- name: Run markduplicates starting from BAM
- command: nextflow run main.nf -profile test_cache,markduplicates_bam --outdir results
+ command: nextflow run main.nf -profile test,markduplicates_bam --outdir results
tags:
- input_bam
- gatk4/markduplicates
@@ -25,32 +25,22 @@
- path: results/reports/markduplicates/test/test.md.cram.metrics
contains: ["testN 0 2820 2 2 0 828 0 0.293617 3807", "1.0 0.999986 1178 1178", "100.0 1.911145 0 0"]
- path: results/reports/mosdepth/test/test.md.mosdepth.global.dist.txt
- md5sum: 8e875e20e3fb9cf288d68c1d223f6fd5
- path: results/reports/mosdepth/test/test.md.mosdepth.region.dist.txt
- md5sum: 75e1ce7e55af51f4985fa91654a5ea2d
- path: results/reports/mosdepth/test/test.md.mosdepth.summary.txt
- md5sum: b23cf96942b2ada3f41172a9349a1175
- path: results/reports/mosdepth/test/test.md.regions.bed.gz
- # binary changes md5sums on reruns
- path: results/reports/mosdepth/test/test.md.regions.bed.gz.csi
- # binary changes md5sums on reruns
- path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt
- md5sum: 8e875e20e3fb9cf288d68c1d223f6fd5
- path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt
- md5sum: 75e1ce7e55af51f4985fa91654a5ea2d
- path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt
- md5sum: b23cf96942b2ada3f41172a9349a1175
- path: results/reports/mosdepth/test/test.recal.regions.bed.gz
- # binary changes md5sums on reruns
- path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi
- # binary changes md5sums on reruns
- path: results/reports/samtools/test/test.md.cram.stats
# conda changes md5sums for test
- path: results/reports/samtools/test/test.recal.cram.stats
# conda changes md5sums for test
- name: Run skip markduplicates bam from step markduplicates
- command: nextflow run main.nf -profile test_cache,markduplicates_bam,skip_markduplicates --outdir results
+ command: nextflow run main.nf -profile test,markduplicates_bam,skip_markduplicates --outdir results
tags:
- input_bam
- markduplicates
@@ -71,25 +61,15 @@
- path: results/preprocessing/recalibrated/test/test.recal.cram.crai
# binary changes md5sums on reruns
- path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt
- md5sum: bdb8f185c35dd1eec7ce2f69bce57972
- path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt
- md5sum: 6fd2e5c5c938bf69cdb2811f9e3afef8
- path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt
- md5sum: 32ea70ef1b99def3dc900b4afd513a40
- path: results/reports/mosdepth/test/test.recal.regions.bed.gz
- md5sum: d034a60ae5c0768d67b9ba6442bd2212
- path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi
- md5sum: b3716e5cd1744610e69c29bd4ffad259
- path: results/reports/mosdepth/test/test.sorted.mosdepth.global.dist.txt
- md5sum: bdb8f185c35dd1eec7ce2f69bce57972
- path: results/reports/mosdepth/test/test.sorted.mosdepth.region.dist.txt
- md5sum: 6fd2e5c5c938bf69cdb2811f9e3afef8
- path: results/reports/mosdepth/test/test.sorted.mosdepth.summary.txt
- md5sum: 32ea70ef1b99def3dc900b4afd513a40
- path: results/reports/mosdepth/test/test.sorted.regions.bed.gz
- md5sum: d034a60ae5c0768d67b9ba6442bd2212
- path: results/reports/mosdepth/test/test.sorted.regions.bed.gz.csi
- md5sum: b3716e5cd1744610e69c29bd4ffad259
- path: results/reports/samtools/test/test.recal.cram.stats
# conda changes md5sums for test
- path: results/reports/samtools/test/test.sorted.cram.stats
diff --git a/tests/test_markduplicates_from_cram.yml b/tests/test_markduplicates_from_cram.yml
index f36619f719..ff28636112 100644
--- a/tests/test_markduplicates_from_cram.yml
+++ b/tests/test_markduplicates_from_cram.yml
@@ -1,5 +1,5 @@
- name: Run markduplicates starting from CRAM
- command: nextflow run main.nf -profile test_cache,markduplicates_cram --outdir results
+ command: nextflow run main.nf -profile test,markduplicates_cram --outdir results
tags:
- input_cram
- gatk4/markduplicates
@@ -25,25 +25,15 @@
- path: results/reports/markduplicates/test/test.md.cram.metrics
contains: ["testN 0 2820 2 2 0 828 0 0.293617 3807", "1.0 0.999986 1178 1178", "100.0 1.911145 0 0"]
- path: results/reports/mosdepth/test/test.md.mosdepth.global.dist.txt
- md5sum: 8e875e20e3fb9cf288d68c1d223f6fd5
- path: results/reports/mosdepth/test/test.md.mosdepth.region.dist.txt
- md5sum: 75e1ce7e55af51f4985fa91654a5ea2d
- path: results/reports/mosdepth/test/test.md.mosdepth.summary.txt
- md5sum: b23cf96942b2ada3f41172a9349a1175
- path: results/reports/mosdepth/test/test.md.regions.bed.gz
- # binary changes md5sums on reruns
- path: results/reports/mosdepth/test/test.md.regions.bed.gz.csi
- # binary changes md5sums on reruns
- path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt
- md5sum: 8e875e20e3fb9cf288d68c1d223f6fd5
- path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt
- md5sum: 75e1ce7e55af51f4985fa91654a5ea2d
- path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt
- md5sum: b23cf96942b2ada3f41172a9349a1175
- path: results/reports/mosdepth/test/test.recal.regions.bed.gz
- # binary changes md5sums on reruns
- path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi
- # binary changes md5sums on reruns
- path: results/reports/samtools/test/test.md.cram.stats
# conda changes md5sums for test
- path: results/reports/samtools/test/test.recal.cram.stats
@@ -51,7 +41,7 @@
- path: results/preprocessing/mapped/
should_exist: false
- name: Run skip markduplicates cram from step markduplicates
- command: nextflow run main.nf -profile test_cache,markduplicates_cram,skip_markduplicates --outdir results
+ command: nextflow run main.nf -profile test,markduplicates_cram,skip_markduplicates --outdir results
tags:
- input_cram
- markduplicates
@@ -68,25 +58,15 @@
- path: results/preprocessing/recalibrated/test/test.recal.cram.crai
# binary changes md5sums on reruns
- path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt
- md5sum: bdb8f185c35dd1eec7ce2f69bce57972
- path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt
- md5sum: 6fd2e5c5c938bf69cdb2811f9e3afef8
- path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt
- md5sum: 32ea70ef1b99def3dc900b4afd513a40
- path: results/reports/mosdepth/test/test.recal.regions.bed.gz
- md5sum: d034a60ae5c0768d67b9ba6442bd2212
- path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi
- md5sum: b3716e5cd1744610e69c29bd4ffad259
- path: results/reports/mosdepth/test/test.sorted.mosdepth.global.dist.txt
- md5sum: bdb8f185c35dd1eec7ce2f69bce57972
- path: results/reports/mosdepth/test/test.sorted.mosdepth.region.dist.txt
- md5sum: 6fd2e5c5c938bf69cdb2811f9e3afef8
- path: results/reports/mosdepth/test/test.sorted.mosdepth.summary.txt
- md5sum: 32ea70ef1b99def3dc900b4afd513a40
- path: results/reports/mosdepth/test/test.sorted.regions.bed.gz
- md5sum: d034a60ae5c0768d67b9ba6442bd2212
- path: results/reports/mosdepth/test/test.sorted.regions.bed.gz.csi
- md5sum: b3716e5cd1744610e69c29bd4ffad259
- path: results/reports/samtools/test/test.recal.cram.stats
# conda changes md5sums for test
- path: results/reports/samtools/test/test.sorted.cram.stats
diff --git a/tests/test_mpileup.yml b/tests/test_mpileup.yml
index f7c5d87749..c6603211b3 100644
--- a/tests/test_mpileup.yml
+++ b/tests/test_mpileup.yml
@@ -1,5 +1,5 @@
- name: Run variant calling on tumor_only sample to test mpileup
- command: nextflow run main.nf -profile test_cache,tools_tumoronly --tools mpileup --outdir results
+ command: nextflow run main.nf -profile test,tools_tumoronly --tools mpileup --outdir results
tags:
- tumor_only
- mpileup
@@ -14,18 +14,13 @@
- path: results/mpileup
should_exist: false
- path: results/reports/mosdepth/sample2/sample2.recal.mosdepth.global.dist.txt
- md5sum: f2dcd00a64947c49e8e4b93c2f4fbf27
- path: results/reports/mosdepth/sample2/sample2.recal.mosdepth.region.dist.txt
- md5sum: 39005ffaac22871ffaaf19656fe69c5b
- path: results/reports/mosdepth/sample2/sample2.recal.mosdepth.summary.txt
- md5sum: 68d4b98f17361fddf73052ead34fa370
- path: results/reports/mosdepth/sample2/sample2.recal.regions.bed.gz
- md5sum: 2819e995eafded35f53328c4ec19ba58
- path: results/reports/mosdepth/sample2/sample2.recal.regions.bed.gz.csi
- md5sum: 393c2749068304d8545b501b9d4658e4
- path: results/reports/samtools/sample2/sample2.recal.cram.stats
- name: Run variant calling on tumor_only sample to test mpileup without intervals
- command: nextflow run main.nf -profile test_cache,tools_tumoronly --tools mpileup --no_intervals --outdir results
+ command: nextflow run main.nf -profile test,tools_tumoronly --tools mpileup --no_intervals --outdir results
tags:
- tumor_only
- mpileup
@@ -47,16 +42,12 @@
- path: results/mpileup
should_exist: false
- path: results/reports/mosdepth/sample2/sample2.recal.mosdepth.global.dist.txt
- md5sum: f2dcd00a64947c49e8e4b93c2f4fbf27
- path: results/reports/mosdepth/sample2/sample2.recal.mosdepth.summary.txt
- md5sum: 0a7300e56eda6fba7c7564f00aa000f0
- path: results/reports/mosdepth/sample2/sample2.recal.per-base.bed.gz
- md5sum: 3de4a9f4da2f2b4909ef192452a8d211
- path: results/reports/mosdepth/sample2/sample2.recal.per-base.bed.gz.csi
- md5sum: cfb07b0ba46e8468b4342edb243536f3
- path: results/reports/samtools/sample2/sample2.recal.cram.stats
- name: Run variant calling on germline sample to test mpileup
- command: nextflow run main.nf -profile test_cache,tools_germline --tools mpileup --outdir results
+ command: nextflow run main.nf -profile test,tools_germline --tools mpileup --outdir results
tags:
- germline
- mpileup
@@ -71,18 +62,13 @@
- path: results/mpileup
should_exist: false
- path: results/reports/mosdepth/sample1/sample1.recal.mosdepth.global.dist.txt
- md5sum: 69e29702ef01fd8f6c7a5468fc35a16a
- path: results/reports/mosdepth/sample1/sample1.recal.mosdepth.region.dist.txt
- md5sum: 6ec49cd7d510c2eb3d9d90fdb79b783a
- path: results/reports/mosdepth/sample1/sample1.recal.mosdepth.summary.txt
- md5sum: 103098d0bf76ed82d2b87d5f242b099a
- path: results/reports/mosdepth/sample1/sample1.recal.regions.bed.gz
- md5sum: b5888cf7395c57d39879a5faa6159eb3
- path: results/reports/mosdepth/sample1/sample1.recal.regions.bed.gz.csi
- md5sum: 9cb0ad7039a3b703d16ca7d5b835c0ee
- path: results/reports/samtools/sample1/sample1.recal.cram.stats
- name: Run variant calling on germline sample to test mpileup without intervals
- command: nextflow run main.nf -profile test_cache,tools_germline --tools mpileup --no_intervals --outdir results
+ command: nextflow run main.nf -profile test,tools_germline --tools mpileup --no_intervals --outdir results
tags:
- germline
- mpileup
@@ -104,11 +90,7 @@
- path: results/mpileup
should_exist: false
- path: results/reports/mosdepth/sample1/sample1.recal.mosdepth.global.dist.txt
- md5sum: 69e29702ef01fd8f6c7a5468fc35a16a
- path: results/reports/mosdepth/sample1/sample1.recal.mosdepth.summary.txt
- md5sum: d2775eb102acc5950f7f53883dcb503d
- path: results/reports/mosdepth/sample1/sample1.recal.per-base.bed.gz
- md5sum: 54431f155c9538809e8caf99d1a75ec7
- path: results/reports/mosdepth/sample1/sample1.recal.per-base.bed.gz.csi
- md5sum: c67dcd711b096eb42f43784d5eadbc0d
- path: results/reports/samtools/sample1/sample1.recal.cram.stats
diff --git a/tests/test_msisensorpro.yml b/tests/test_msisensorpro.yml
index 173dbcf5ca..5133de900b 100644
--- a/tests/test_msisensorpro.yml
+++ b/tests/test_msisensorpro.yml
@@ -1,5 +1,5 @@
- name: Run variant calling on somatic sample with msisensor-pro
- command: nextflow run main.nf -profile test_cache,tools_somatic --tools msisensorpro --outdir results
+ command: nextflow run main.nf -profile test,tools_somatic --tools msisensorpro --outdir results
tags:
- msisensorpro
- somatic
@@ -13,31 +13,21 @@
- path: results/msisensorpro
should_exist: false
- path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.global.dist.txt
- md5sum: 69e29702ef01fd8f6c7a5468fc35a16a
- path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.region.dist.txt
- md5sum: 6ec49cd7d510c2eb3d9d90fdb79b783a
- path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.summary.txt
- md5sum: 103098d0bf76ed82d2b87d5f242b099a
- path: results/reports/mosdepth/sample3/sample3.recal.regions.bed.gz
- md5sum: b5888cf7395c57d39879a5faa6159eb3
- path: results/reports/mosdepth/sample3/sample3.recal.regions.bed.gz.csi
- md5sum: 9cb0ad7039a3b703d16ca7d5b835c0ee
- path: results/reports/samtools/sample3/sample3.recal.cram.stats
# conda changes md5sums for test
- path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.global.dist.txt
- md5sum: f2dcd00a64947c49e8e4b93c2f4fbf27
- path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.region.dist.txt
- md5sum: 39005ffaac22871ffaaf19656fe69c5b
- path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.summary.txt
- md5sum: 68d4b98f17361fddf73052ead34fa370
- path: results/reports/mosdepth/sample4/sample4.recal.regions.bed.gz
- md5sum: 2819e995eafded35f53328c4ec19ba58
- path: results/reports/mosdepth/sample4/sample4.recal.regions.bed.gz.csi
- md5sum: 393c2749068304d8545b501b9d4658e4
- path: results/reports/samtools/sample4/sample4.recal.cram.stats
# conda changes md5sums for test
- name: Build only index with msisensorpro
- command: nextflow run main.nf -profile test_cache --build_only_index --tools msisensorpro --input false --outdir results
+ command: nextflow run main.nf -profile test --build_only_index --tools msisensorpro --input false --outdir results
tags:
- build_only_index
- msisensorpro
@@ -53,19 +43,11 @@
md5sum: 8569fbdb2c98c6fb16dfa73d8eacb070
- path: results/reference/bwa/genome.sa
md5sum: e7cff62b919448a3a3d0fe4aaf427594
- - path: results/reference/dbsnp/dbsnp_146.hg38.vcf.gz.tbi
- # conda changes md5sums for test
- - path: results/reference/dict/genome.dict
- md5sum: 2433fe2ba31257337bf4c4bd4cb8da15
- - path: results/reference/fai/genome.fasta.fai
- md5sum: 3520cd30e1b100e55f578db9c855f685
- path: results/reference/intervals/chr22_1-40001.bed
md5sum: 87a15eb9c2ff20ccd5cd8735a28708f7
- path: results/reference/intervals/chr22_1-40001.bed.gz
md5sum: d3341fa28986c40b24fcc10a079dbb80
- path: results/reference/intervals/genome.bed
md5sum: a87dc7d20ebca626f65cc16ff6c97a3e
- - path: results/reference/known_indels/mills_and_1000G.indels.vcf.gz.tbi
- # conda changes md5sums for test
- path: results/reference/msi/genome.msisensor_scan.list
md5sum: a7886e7a56a1d7e3be6b4496753fd743
diff --git a/tests/test_mutect2.yml b/tests/test_mutect2.yml
index 52b422b1bf..c5ea0e8b8d 100644
--- a/tests/test_mutect2.yml
+++ b/tests/test_mutect2.yml
@@ -1,5 +1,5 @@
- name: Run variant calling on tumor only sample with mutect2
- command: nextflow run main.nf -profile test_cache,tools_tumoronly --tools mutect2 --outdir results
+ command: nextflow run main.nf -profile test,tools_tumoronly --tools mutect2 --outdir results
tags:
- mutect2
- tumor_only
@@ -39,18 +39,13 @@
- path: results/mutect2
should_exist: false
- path: results/reports/mosdepth/sample2/sample2.recal.mosdepth.global.dist.txt
- md5sum: f2dcd00a64947c49e8e4b93c2f4fbf27
- path: results/reports/mosdepth/sample2/sample2.recal.mosdepth.region.dist.txt
- md5sum: 39005ffaac22871ffaaf19656fe69c5b
- path: results/reports/mosdepth/sample2/sample2.recal.mosdepth.summary.txt
- md5sum: 68d4b98f17361fddf73052ead34fa370
- path: results/reports/mosdepth/sample2/sample2.recal.regions.bed.gz
- md5sum: 2819e995eafded35f53328c4ec19ba58
- path: results/reports/mosdepth/sample2/sample2.recal.regions.bed.gz.csi
- md5sum: 393c2749068304d8545b501b9d4658e4
- path: results/reports/samtools/sample2/sample2.recal.cram.stats
- name: Run variant calling on tumor only sample with mutect2 without intervals
- command: nextflow run main.nf -profile test_cache,tools_tumoronly --tools mutect2 --no_intervals --outdir results
+ command: nextflow run main.nf -profile test,tools_tumoronly --tools mutect2 --no_intervals --outdir results
tags:
- mutect2
- no_intervals
@@ -97,11 +92,7 @@
- path: results/mutect2
should_exist: false
- path: results/reports/mosdepth/sample2/sample2.recal.mosdepth.global.dist.txt
- md5sum: f2dcd00a64947c49e8e4b93c2f4fbf27
- path: results/reports/mosdepth/sample2/sample2.recal.mosdepth.summary.txt
- md5sum: 0a7300e56eda6fba7c7564f00aa000f0
- path: results/reports/mosdepth/sample2/sample2.recal.per-base.bed.gz
- md5sum: 3de4a9f4da2f2b4909ef192452a8d211
- path: results/reports/mosdepth/sample2/sample2.recal.per-base.bed.gz.csi
- md5sum: cfb07b0ba46e8468b4342edb243536f3
- path: results/reports/samtools/sample2/sample2.recal.cram.stats
diff --git a/tests/test_ngscheckmate.yml b/tests/test_ngscheckmate.yml
index 8923ddc9ec..b48a62b629 100644
--- a/tests/test_ngscheckmate.yml
+++ b/tests/test_ngscheckmate.yml
@@ -1,5 +1,5 @@
- name: Check ngscheckmate is working
- command: nextflow run main.nf -profile test_cache,tools --tools ngscheckmate --outdir results
+ command: nextflow run main.nf -profile test,tools --tools ngscheckmate --outdir results
tags:
- ngscheckmate
- tools
diff --git a/tests/test_prepare_recalibration_from_bam.yml b/tests/test_prepare_recalibration_from_bam.yml
index 3d2560058c..335a67deed 100644
--- a/tests/test_prepare_recalibration_from_bam.yml
+++ b/tests/test_prepare_recalibration_from_bam.yml
@@ -1,5 +1,5 @@
- name: Run prepare_recalibration starting from bam
- command: nextflow run main.nf -profile test_cache,prepare_recalibration_bam --outdir results
+ command: nextflow run main.nf -profile test,prepare_recalibration_bam --outdir results
tags:
- input_bam
- prepare_recalibration
@@ -21,15 +21,10 @@
- path: results/preprocessing/recalibrated/test/test.recal.cram.crai
# binary changes md5sums on reruns
- path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt
- md5sum: bdb8f185c35dd1eec7ce2f69bce57972
- path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt
- md5sum: 6fd2e5c5c938bf69cdb2811f9e3afef8
- path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt
- md5sum: 32ea70ef1b99def3dc900b4afd513a40
- path: results/reports/mosdepth/test/test.recal.regions.bed.gz
- md5sum: d034a60ae5c0768d67b9ba6442bd2212
- path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi
- md5sum: b3716e5cd1744610e69c29bd4ffad259
- path: results/reports/samtools/test/test.recal.cram.stats
# conda changes md5sums for test
- path: results/preprocessing/mapped/
@@ -37,7 +32,7 @@
- path: results/preprocessing/markduplicates/
should_exist: false
- name: Run prepare_recalibration starting from bam and skip baserecalibration
- command: nextflow run main.nf -profile test_cache,prepare_recalibration_bam,skip_bqsr --tools strelka --outdir results
+ command: nextflow run main.nf -profile test,prepare_recalibration_bam,skip_bqsr --tools strelka --outdir results
tags:
- input_bam
- prepare_recalibration
diff --git a/tests/test_prepare_recalibration_from_cram.yml b/tests/test_prepare_recalibration_from_cram.yml
index d69fa91525..6e362ccd7b 100644
--- a/tests/test_prepare_recalibration_from_cram.yml
+++ b/tests/test_prepare_recalibration_from_cram.yml
@@ -1,5 +1,5 @@
- name: Run prepare_recalibration starting from cram
- command: nextflow run main.nf -profile test_cache,prepare_recalibration_cram --outdir results
+ command: nextflow run main.nf -profile test,prepare_recalibration_cram --outdir results
tags:
- input_cram
- prepare_recalibration
@@ -15,15 +15,10 @@
- path: results/preprocessing/recalibrated/test/test.recal.cram.crai
# binary changes md5sums on reruns
- path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt
- md5sum: bdb8f185c35dd1eec7ce2f69bce57972
- path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt
- md5sum: 6fd2e5c5c938bf69cdb2811f9e3afef8
- path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt
- md5sum: 32ea70ef1b99def3dc900b4afd513a40
- path: results/reports/mosdepth/test/test.recal.regions.bed.gz
- md5sum: d034a60ae5c0768d67b9ba6442bd2212
- path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi
- md5sum: b3716e5cd1744610e69c29bd4ffad259
- path: results/reports/samtools/test/test.recal.cram.stats
# conda changes md5sums for test
- path: results/preprocessing/mapped/
@@ -31,7 +26,7 @@
- path: results/preprocessing/markduplicates/
should_exist: false
- name: Run prepare_recalibration starting from cram and skip baserecalibration
- command: nextflow run main.nf -profile test_cache,prepare_recalibration_cram,skip_bqsr --tools strelka --outdir results
+ command: nextflow run main.nf -profile test,prepare_recalibration_cram,skip_bqsr --tools strelka --outdir results
tags:
- input_cram
- prepare_recalibration
diff --git a/tests/test_recalibrate_from_bam.yml b/tests/test_recalibrate_from_bam.yml
index cc1a3e114a..fb96a3d305 100644
--- a/tests/test_recalibrate_from_bam.yml
+++ b/tests/test_recalibrate_from_bam.yml
@@ -1,5 +1,5 @@
- name: Run Recalibration starting from bam
- command: nextflow run main.nf -profile test_cache,recalibrate_bam --outdir results
+ command: nextflow run main.nf -profile test,recalibrate_bam --outdir results
tags:
- input_bam
- recalibrate
@@ -17,15 +17,10 @@
- path: results/preprocessing/recalibrated/test/test.recal.cram.crai
# binary changes md5sums on reruns
- path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt
- md5sum: bdb8f185c35dd1eec7ce2f69bce57972
- path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt
- md5sum: 6fd2e5c5c938bf69cdb2811f9e3afef8
- path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt
- md5sum: 32ea70ef1b99def3dc900b4afd513a40
- path: results/reports/mosdepth/test/test.recal.regions.bed.gz
- md5sum: d034a60ae5c0768d67b9ba6442bd2212
- path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi
- md5sum: b3716e5cd1744610e69c29bd4ffad259
- path: results/reports/samtools/test/test.recal.cram.stats
# conda changes md5sums for test
- path: results/preprocessing/mapped/
@@ -33,7 +28,7 @@
- path: results/preprocessing/markduplicates/
should_exist: false
- name: Run Recalibration starting from bam and skip baserecalibration
- command: nextflow run main.nf -profile test_cache,recalibrate_bam,skip_bqsr --tools strelka --outdir results
+ command: nextflow run main.nf -profile test,recalibrate_bam,skip_bqsr --tools strelka --outdir results
tags:
- input_bam
- recalibrate
diff --git a/tests/test_recalibrate_from_cram.yml b/tests/test_recalibrate_from_cram.yml
index e843424f50..9e53da4f2d 100644
--- a/tests/test_recalibrate_from_cram.yml
+++ b/tests/test_recalibrate_from_cram.yml
@@ -1,5 +1,5 @@
- name: Run Recalibration starting from cram
- command: nextflow run main.nf -profile test_cache,recalibrate_cram --outdir results
+ command: nextflow run main.nf -profile test,recalibrate_cram --outdir results
tags:
- input_cram
- recalibrate
@@ -13,15 +13,10 @@
- path: results/preprocessing/recalibrated/test/test.recal.cram.crai
# binary changes md5sums on reruns
- path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt
- md5sum: bdb8f185c35dd1eec7ce2f69bce57972
- path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt
- md5sum: 6fd2e5c5c938bf69cdb2811f9e3afef8
- path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt
- md5sum: 32ea70ef1b99def3dc900b4afd513a40
- path: results/reports/mosdepth/test/test.recal.regions.bed.gz
- md5sum: d034a60ae5c0768d67b9ba6442bd2212
- path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi
- md5sum: b3716e5cd1744610e69c29bd4ffad259
- path: results/reports/samtools/test/test.recal.cram.stats
# conda changes md5sums for test
- path: results/preprocessing/mapped/
@@ -29,7 +24,7 @@
- path: results/preprocessing/markduplicates/
should_exist: false
- name: Run Recalibration starting from cram and skip baserecalibration
- command: nextflow run main.nf -profile test_cache,recalibrate_cram,skip_bqsr --tools strelka --outdir results
+ command: nextflow run main.nf -profile test,recalibrate_cram,skip_bqsr --tools strelka --outdir results
tags:
- input_cram
- recalibrate
diff --git a/tests/test_samplesheet_validation_spaces.yml b/tests/test_samplesheet_validation_spaces.yml
index edd0576d3a..f0983b0518 100644
--- a/tests/test_samplesheet_validation_spaces.yml
+++ b/tests/test_samplesheet_validation_spaces.yml
@@ -1,5 +1,5 @@
- name: Test that pipeline fail when sample/patient name contain space
- command: nextflow run main.nf -profile test_cache --input ./tests/csv/3.0/sample_with_space.csv --outdir results
+ command: nextflow run main.nf -profile test --input ./tests/csv/3.0/sample_with_space.csv --outdir results
tags:
- sample_with_space
- validation_checks
diff --git a/tests/test_save_mapped.yml b/tests/test_save_mapped.yml
index 7868da9d35..251e7ddacc 100644
--- a/tests/test_save_mapped.yml
+++ b/tests/test_save_mapped.yml
@@ -1,5 +1,5 @@
- name: Run save_mapped
- command: nextflow run main.nf -profile test_cache --save_mapped --outdir results
+ command: nextflow run main.nf -profile test --save_mapped --outdir results
tags:
- default_extended
- preprocessing
@@ -34,25 +34,15 @@
- path: results/reports/markduplicates/test/test.md.cram.metrics
contains: ["test 17094 1534 168 1046782 12429 197 0 0.635998", "1.0 0.999991 1171"]
- path: results/reports/mosdepth/test/test.md.mosdepth.global.dist.txt
- md5sum: b61e1acee11a6ddf7ce3232a5948a6a0
- path: results/reports/mosdepth/test/test.md.mosdepth.region.dist.txt
- md5sum: 1a382f98d488d2ae3df83a0d87caafc1
- path: results/reports/mosdepth/test/test.md.mosdepth.summary.txt
- md5sum: 839108358878ada89e1eaddf6e0541ba
- path: results/reports/mosdepth/test/test.md.regions.bed.gz
- md5sum: 0aaee6da65050bedcd40b9fbf0622873
- path: results/reports/mosdepth/test/test.md.regions.bed.gz.csi
- md5sum: 544e02fcca548749a0af758d0a2df352
- path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt
- md5sum: b61e1acee11a6ddf7ce3232a5948a6a0
- path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt
- md5sum: 1a382f98d488d2ae3df83a0d87caafc1
- path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt
- md5sum: 839108358878ada89e1eaddf6e0541ba
- path: results/reports/mosdepth/test/test.recal.regions.bed.gz
- md5sum: 0aaee6da65050bedcd40b9fbf0622873
- path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi
- md5sum: 544e02fcca548749a0af758d0a2df352
- path: results/reports/samtools/test/test.md.cram.stats
# conda changes md5sums for test
- path: results/reports/samtools/test/test.recal.cram.stats
diff --git a/tests/test_save_output_as_bam_only.yml b/tests/test_save_output_as_bam_only.yml
index bc577c0ae8..6e47260424 100644
--- a/tests/test_save_output_as_bam_only.yml
+++ b/tests/test_save_output_as_bam_only.yml
@@ -1,5 +1,5 @@
- name: Run save_output_as_bam
- command: nextflow run main.nf -profile test_cache --save_output_as_bam --outdir results
+ command: nextflow run main.nf -profile test --save_output_as_bam --outdir results
tags:
- default_extended
- preprocessing
@@ -28,25 +28,15 @@
- path: results/reports/markduplicates/test/test.md.cram.metrics
contains: ["test 17094 1534 168 1046782 12429 197 0 0.635998", "1.0 0.999991 1171"]
- path: results/reports/mosdepth/test/test.md.mosdepth.global.dist.txt
- md5sum: b61e1acee11a6ddf7ce3232a5948a6a0
- path: results/reports/mosdepth/test/test.md.mosdepth.region.dist.txt
- md5sum: 1a382f98d488d2ae3df83a0d87caafc1
- path: results/reports/mosdepth/test/test.md.mosdepth.summary.txt
- md5sum: 839108358878ada89e1eaddf6e0541ba
- path: results/reports/mosdepth/test/test.md.regions.bed.gz
- md5sum: 0aaee6da65050bedcd40b9fbf0622873
- path: results/reports/mosdepth/test/test.md.regions.bed.gz.csi
- md5sum: 544e02fcca548749a0af758d0a2df352
- path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt
- md5sum: b61e1acee11a6ddf7ce3232a5948a6a0
- path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt
- md5sum: 1a382f98d488d2ae3df83a0d87caafc1
- path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt
- md5sum: 839108358878ada89e1eaddf6e0541ba
- path: results/reports/mosdepth/test/test.recal.regions.bed.gz
- md5sum: 0aaee6da65050bedcd40b9fbf0622873
- path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi
- md5sum: 544e02fcca548749a0af758d0a2df352
- path: results/reports/samtools/test/test.md.cram.stats
# conda changes md5sums for test
- path: results/reports/samtools/test/test.recal.cram.stats
diff --git a/tests/test_sentieon_aligner_bwamem.yml b/tests/test_sentieon_aligner_bwamem.yml
index 37f883312d..36f5e66683 100644
--- a/tests/test_sentieon_aligner_bwamem.yml
+++ b/tests/test_sentieon_aligner_bwamem.yml
@@ -1,5 +1,5 @@
- name: Run sentieon bwamem
- command: nextflow run main.nf -profile test_cache,software_license --sentieon_extension --aligner sentieon-bwamem --save_reference --outdir results
+ command: nextflow run main.nf -profile test,software_license --sentieon_extension --aligner sentieon-bwamem --save_reference --outdir results
tags:
- aligner
- sentieon/bwamem
@@ -50,31 +50,21 @@
- path: results/reports/markduplicates/test/test.md.cram.metrics
contains: ["test 17094 1534 168 1046782 12429 197 0 0.635998", "1.0 0.999991 1171"]
- path: results/reports/mosdepth/test/test.md.mosdepth.global.dist.txt
- md5sum: b61e1acee11a6ddf7ce3232a5948a6a0
- path: results/reports/mosdepth/test/test.md.mosdepth.region.dist.txt
- md5sum: 1a382f98d488d2ae3df83a0d87caafc1
- path: results/reports/mosdepth/test/test.md.mosdepth.summary.txt
- md5sum: 9afbcd5e44b62b3947e47af850a66188
- path: results/reports/mosdepth/test/test.md.regions.bed.gz
- md5sum: 3bd6a6f7127394802d9a7c7d559072ee
- path: results/reports/mosdepth/test/test.md.regions.bed.gz.csi
- md5sum: 72ae14370dfdaab906e50d0552c90119
- path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt
- md5sum: b61e1acee11a6ddf7ce3232a5948a6a0
- path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt
- md5sum: 1a382f98d488d2ae3df83a0d87caafc1
- path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt
- md5sum: 9afbcd5e44b62b3947e47af850a66188
- path: results/reports/mosdepth/test/test.recal.regions.bed.gz
- md5sum: 3bd6a6f7127394802d9a7c7d559072ee
- path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi
- md5sum: 72ae14370dfdaab906e50d0552c90119
- path: results/reports/samtools/test/test.md.cram.stats
# conda changes md5sums for test
- path: results/reports/samtools/test/test.recal.cram.stats
# conda changes md5sums for test
- name: Build only index with sentieon bwa
- command: nextflow run main.nf -profile test_cache,software_license --sentieon_extension --aligner sentieon-bwamem --build_only_index --outdir results
+ command: nextflow run main.nf -profile test,software_license --sentieon_extension --aligner sentieon-bwamem --build_only_index --outdir results
tags:
- aligner
- build_only_index
@@ -106,7 +96,7 @@
- path: results/reference/known_indels/mills_and_1000G.indels.vcf.gz.tbi
# conda changes md5sums for test
- name: Run sentieon bwamem save bam
- command: nextflow run main.nf -profile test_cache,software_license --sentieon_extension --aligner sentieon-bwamem --save_mapped --save_output_as_bam --outdir results
+ command: nextflow run main.nf -profile test,software_license --sentieon_extension --aligner sentieon-bwamem --save_mapped --save_output_as_bam --outdir results
tags:
- aligner
- sentieon/bwamem
@@ -136,31 +126,21 @@
- path: results/reports/markduplicates/test/test.md.cram.metrics
contains: ["test 17094 1534 168 1046782 12429 197 0 0.635998", "1.0 0.999991 1171"]
- path: results/reports/mosdepth/test/test.md.mosdepth.global.dist.txt
- md5sum: b61e1acee11a6ddf7ce3232a5948a6a0
- path: results/reports/mosdepth/test/test.md.mosdepth.region.dist.txt
- md5sum: 1a382f98d488d2ae3df83a0d87caafc1
- path: results/reports/mosdepth/test/test.md.mosdepth.summary.txt
- md5sum: 9afbcd5e44b62b3947e47af850a66188
- path: results/reports/mosdepth/test/test.md.regions.bed.gz
- md5sum: 3bd6a6f7127394802d9a7c7d559072ee
- path: results/reports/mosdepth/test/test.md.regions.bed.gz.csi
- md5sum: 72ae14370dfdaab906e50d0552c90119
- path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt
- md5sum: b61e1acee11a6ddf7ce3232a5948a6a0
- path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt
- md5sum: 1a382f98d488d2ae3df83a0d87caafc1
- path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt
- md5sum: 9afbcd5e44b62b3947e47af850a66188
- path: results/reports/mosdepth/test/test.recal.regions.bed.gz
- md5sum: 3bd6a6f7127394802d9a7c7d559072ee
- path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi
- md5sum: 72ae14370dfdaab906e50d0552c90119
- path: results/reports/samtools/test/test.md.cram.stats
# conda changes md5sums for test
- path: results/reports/samtools/test/test.recal.cram.stats
# conda changes md5sums for test
- name: Run sentieon bwamem save cram
- command: nextflow run main.nf -profile test_cache,software_license --sentieon_extension --aligner sentieon-bwamem --save_mapped --outdir results
+ command: nextflow run main.nf -profile test,software_license --sentieon_extension --aligner sentieon-bwamem --save_mapped --outdir results
tags:
- aligner
- sentieon/bwamem
@@ -190,25 +170,15 @@
- path: results/reports/markduplicates/test/test.md.cram.metrics
contains: ["test 17094 1534 168 1046782 12429 197 0 0.635998", "1.0 0.999991 1171"]
- path: results/reports/mosdepth/test/test.md.mosdepth.global.dist.txt
- md5sum: b61e1acee11a6ddf7ce3232a5948a6a0
- path: results/reports/mosdepth/test/test.md.mosdepth.region.dist.txt
- md5sum: 1a382f98d488d2ae3df83a0d87caafc1
- path: results/reports/mosdepth/test/test.md.mosdepth.summary.txt
- md5sum: 9afbcd5e44b62b3947e47af850a66188
- path: results/reports/mosdepth/test/test.md.regions.bed.gz
- md5sum: 3bd6a6f7127394802d9a7c7d559072ee
- path: results/reports/mosdepth/test/test.md.regions.bed.gz.csi
- md5sum: 72ae14370dfdaab906e50d0552c90119
- path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt
- md5sum: b61e1acee11a6ddf7ce3232a5948a6a0
- path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt
- md5sum: 1a382f98d488d2ae3df83a0d87caafc1
- path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt
- md5sum: 9afbcd5e44b62b3947e47af850a66188
- path: results/reports/mosdepth/test/test.recal.regions.bed.gz
- md5sum: 3bd6a6f7127394802d9a7c7d559072ee
- path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi
- md5sum: 72ae14370dfdaab906e50d0552c90119
- path: results/reports/samtools/test/test.md.cram.stats
# conda changes md5sums for test
- path: results/reports/samtools/test/test.recal.cram.stats
diff --git a/tests/test_sentieon_dedup_from_bam.yml b/tests/test_sentieon_dedup_from_bam.yml
index 54df60e415..48d55177e0 100644
--- a/tests/test_sentieon_dedup_from_bam.yml
+++ b/tests/test_sentieon_dedup_from_bam.yml
@@ -1,5 +1,5 @@
- name: Run sentieon dedup starting from BAM
- command: nextflow run main.nf -profile test_cache,software_license,sentieon_dedup_bam --sentieon_extension --outdir results
+ command: nextflow run main.nf -profile test,software_license,sentieon_dedup_bam --sentieon_extension --outdir results
tags:
- input_bam
- preprocessing
@@ -27,25 +27,15 @@
- path: results/reports/sentieon_dedup/test/test.dedup.cram.metrics
contains: ["testN 0 2820 2 2 0 828 0 0.293617 3807", "1.0 0.999986", "100.0 1.911145"]
- path: results/reports/mosdepth/test/test.dedup.mosdepth.global.dist.txt
- md5sum: 8e875e20e3fb9cf288d68c1d223f6fd5
- path: results/reports/mosdepth/test/test.dedup.mosdepth.region.dist.txt
- md5sum: 75e1ce7e55af51f4985fa91654a5ea2d
- path: results/reports/mosdepth/test/test.dedup.mosdepth.summary.txt
- md5sum: b23cf96942b2ada3f41172a9349a1175
- path: results/reports/mosdepth/test/test.dedup.regions.bed.gz
- # binary changes md5sums on reruns
- path: results/reports/mosdepth/test/test.dedup.regions.bed.gz.csi
- # binary changes md5sums on reruns
- path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt
- md5sum: 8e875e20e3fb9cf288d68c1d223f6fd5
- path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt
- md5sum: 75e1ce7e55af51f4985fa91654a5ea2d
- path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt
- md5sum: b23cf96942b2ada3f41172a9349a1175
- path: results/reports/mosdepth/test/test.recal.regions.bed.gz
- # binary changes md5sums on reruns
- path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi
- # binary changes md5sums on reruns
- path: results/reports/samtools/test/test.dedup.cram.stats
# conda changes md5sums for test
- path: results/reports/samtools/test/test.recal.cram.stats
diff --git a/tests/test_sentieon_dedup_from_cram.yml b/tests/test_sentieon_dedup_from_cram.yml
index 87dfdebfa7..9f826c502c 100644
--- a/tests/test_sentieon_dedup_from_cram.yml
+++ b/tests/test_sentieon_dedup_from_cram.yml
@@ -1,5 +1,5 @@
- name: Run sentieon dedup starting from CRAM
- command: nextflow run main.nf -profile test_cache,software_license,sentieon_dedup_cram --sentieon_extension --outdir results
+ command: nextflow run main.nf -profile test,software_license,sentieon_dedup_cram --sentieon_extension --outdir results
tags:
- input_cram
- preprocessing
@@ -27,25 +27,15 @@
- path: results/reports/sentieon_dedup/test/test.dedup.cram.metrics
contains: ["testN 0 2820 2 2 0 828 0 0.293617 3807", "1.0 0.999986", "2.0 1.476740", "3.0 1.704038"]
- path: results/reports/mosdepth/test/test.dedup.mosdepth.global.dist.txt
- md5sum: 8e875e20e3fb9cf288d68c1d223f6fd5
- path: results/reports/mosdepth/test/test.dedup.mosdepth.region.dist.txt
- md5sum: 75e1ce7e55af51f4985fa91654a5ea2d
- path: results/reports/mosdepth/test/test.dedup.mosdepth.summary.txt
- md5sum: b23cf96942b2ada3f41172a9349a1175
- path: results/reports/mosdepth/test/test.dedup.regions.bed.gz
- # binary changes md5sums on reruns
- path: results/reports/mosdepth/test/test.dedup.regions.bed.gz.csi
- # binary changes md5sums on reruns
- path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt
- md5sum: 8e875e20e3fb9cf288d68c1d223f6fd5
- path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt
- md5sum: 75e1ce7e55af51f4985fa91654a5ea2d
- path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt
- md5sum: b23cf96942b2ada3f41172a9349a1175
- path: results/reports/mosdepth/test/test.recal.regions.bed.gz
- # binary changes md5sums on reruns
- path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi
- # binary changes md5sums on reruns
- path: results/reports/samtools/test/test.dedup.cram.stats
# conda changes md5sums for test
- path: results/reports/samtools/test/test.recal.cram.stats
diff --git a/tests/test_sentieon_dnascope.yml b/tests/test_sentieon_dnascope.yml
index 49b88ca43c..142cd73156 100644
--- a/tests/test_sentieon_dnascope.yml
+++ b/tests/test_sentieon_dnascope.yml
@@ -1,5 +1,5 @@
- name: Run variant calling on germline sample with sentieons dnascope
- command: nextflow run main.nf -profile test_cache,targeted,software_license --sentieon_extension --input ./tests/csv/3.0/mapped_single_bam.csv --tools sentieon_dnascope --step variant_calling --outdir results
+ command: nextflow run main.nf -profile test,targeted,software_license --sentieon_extension --input ./tests/csv/3.0/mapped_single_bam.csv --tools sentieon_dnascope --step variant_calling --outdir results
tags:
- germline
- sentieon/dnascope
@@ -34,18 +34,13 @@
- path: results/dnascope
should_exist: false
- path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt
- md5sum: e82e90c7d508a135b5a8a7cd6933452e
- path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt
- md5sum: 3a2030e5e8af7bc12720c3a5592bf921
- path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt
- md5sum: 615c5c5019d88045a9ff5bbe6e63d270
- path: results/reports/mosdepth/test/test.recal.regions.bed.gz
- md5sum: 9f1ea20e7461db948ba21f70c4d1b3ba
- path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi
- md5sum: 5c00a1d457c387d6e71848a6d897e309
- path: results/reports/samtools/test/test.recal.cram.stats
- name: Run variant calling on germline sample with sentieons dnascope without intervals
- command: nextflow run main.nf -profile test_cache,targeted,software_license --sentieon_extension --input ./tests/csv/3.0/mapped_single_bam.csv --tools sentieon_dnascope --step variant_calling --no_intervals --outdir results
+ command: nextflow run main.nf -profile test,targeted,software_license --sentieon_extension --input ./tests/csv/3.0/mapped_single_bam.csv --tools sentieon_dnascope --step variant_calling --no_intervals --outdir results
tags:
- germline
- sentieon/dnascope
@@ -87,17 +82,13 @@
- path: results/sentieon_dnascope
should_exist: false
- path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt
- md5sum: e82e90c7d508a135b5a8a7cd6933452e
- path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt
- md5sum: 4f0d231060cbde4efdd673863bd2fb59
- path: results/reports/mosdepth/test/test.recal.per-base.bed.gz
- md5sum: bc1df47d46f818fee5275975925d769a
- path: results/reports/mosdepth/test/test.recal.per-base.bed.gz.csi
- md5sum: 9e649ac749ff6c6073bef5ab63e8aaa4
- path: results/reports/samtools/test/test.recal.cram.stats
- name: Run variant calling on germline sample with sentieons dnascope output gvcf
- command: nextflow run main.nf -profile test_cache,targeted,software_license --sentieon_extension --input ./tests/csv/3.0/mapped_single_bam.csv --tools sentieon_dnascope --step variant_calling --outdir results --sentieon_dnascope_emit_mode gvcf
+ command: nextflow run main.nf -profile test,targeted,software_license --sentieon_extension --input ./tests/csv/3.0/mapped_single_bam.csv --tools sentieon_dnascope --step variant_calling --outdir results --sentieon_dnascope_emit_mode gvcf
tags:
- germline
- sentieon/dnascope
@@ -135,18 +126,13 @@
- path: results/dnascope
should_exist: false
- path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt
- md5sum: e82e90c7d508a135b5a8a7cd6933452e
- path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt
- md5sum: 3a2030e5e8af7bc12720c3a5592bf921
- path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt
- md5sum: 615c5c5019d88045a9ff5bbe6e63d270
- path: results/reports/mosdepth/test/test.recal.regions.bed.gz
- md5sum: 9f1ea20e7461db948ba21f70c4d1b3ba
- path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi
- md5sum: 5c00a1d457c387d6e71848a6d897e309
- path: results/reports/samtools/test/test.recal.cram.stats
- name: Run variant calling on germline sample with sentieons dnascope output both gvcf and vcf
- command: nextflow run main.nf -profile test_cache,targeted,software_license --sentieon_extension --input ./tests/csv/3.0/mapped_single_bam.csv --tools sentieon_dnascope --step variant_calling --outdir results --sentieon_dnascope_emit_mode variant,gvcf
+ command: nextflow run main.nf -profile test,targeted,software_license --sentieon_extension --input ./tests/csv/3.0/mapped_single_bam.csv --tools sentieon_dnascope --step variant_calling --outdir results --sentieon_dnascope_emit_mode variant,gvcf
tags:
- germline
- sentieon/dnascope
@@ -176,13 +162,8 @@
- path: results/dnascope
should_exist: false
- path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt
- md5sum: e82e90c7d508a135b5a8a7cd6933452e
- path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt
- md5sum: 3a2030e5e8af7bc12720c3a5592bf921
- path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt
- md5sum: 615c5c5019d88045a9ff5bbe6e63d270
- path: results/reports/mosdepth/test/test.recal.regions.bed.gz
- md5sum: 9f1ea20e7461db948ba21f70c4d1b3ba
- path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi
- md5sum: 5c00a1d457c387d6e71848a6d897e309
- path: results/reports/samtools/test/test.recal.cram.stats
diff --git a/tests/test_sentieon_dnascope_joint_germline.yml b/tests/test_sentieon_dnascope_joint_germline.yml
index d5775cc048..84a217eefe 100644
--- a/tests/test_sentieon_dnascope_joint_germline.yml
+++ b/tests/test_sentieon_dnascope_joint_germline.yml
@@ -1,5 +1,5 @@
- name: Run joint germline variant calling with sentieon dnascope
- command: nextflow run main.nf -profile test_cache,targeted,software_license --sentieon_extension --input ./tests/csv/3.0/mapped_joint_bam.csv --tools sentieon_dnascope --step variant_calling --joint_germline --outdir results --sentieon_dnascope_emit_mode gvcf
+ command: nextflow run main.nf -profile test,targeted,software_license --sentieon_extension --input ./tests/csv/3.0/mapped_joint_bam.csv --tools sentieon_dnascope --step variant_calling --joint_germline --outdir results --sentieon_dnascope_emit_mode gvcf
tags:
- germline
- sentieon/dnascope_joint_germline
@@ -51,7 +51,7 @@
- path: results/reports/mosdepth/testT/testT.recal.regions.bed.gz.csi
- path: results/reports/samtools/testT/testT.recal.cram.stats
- name: Run joint germline variant calling with sentieon dnascope all intervals at once
- command: nextflow run main.nf -profile test_cache,targeted,software_license --sentieon_extension --input ./tests/csv/3.0/mapped_joint_bam.csv --tools sentieon_dnascope --step variant_calling --joint_germline --outdir results --sentieon_dnascope_emit_mode gvcf --nucleotides_per_second 100
+ command: nextflow run main.nf -profile test,targeted,software_license --sentieon_extension --input ./tests/csv/3.0/mapped_joint_bam.csv --tools sentieon_dnascope --step variant_calling --joint_germline --outdir results --sentieon_dnascope_emit_mode gvcf --nucleotides_per_second 100
tags:
- germline
- sentieon/dnascope_joint_germline
diff --git a/tests/test_sentieon_dnascope_skip_filter.yml b/tests/test_sentieon_dnascope_skip_filter.yml
index 3950f7a438..b3740ca749 100644
--- a/tests/test_sentieon_dnascope_skip_filter.yml
+++ b/tests/test_sentieon_dnascope_skip_filter.yml
@@ -1,5 +1,5 @@
- name: Run variant calling on germline sample with sentieon dnascope and skip filter
- command: nextflow run main.nf -profile test_cache,targeted,software_license --sentieon_extension --input ./tests/csv/3.0/mapped_single_bam.csv --tools sentieon_dnascope --step variant_calling --skip_tools dnascope_filter --outdir results
+ command: nextflow run main.nf -profile test,targeted,software_license --sentieon_extension --input ./tests/csv/3.0/mapped_single_bam.csv --tools sentieon_dnascope --step variant_calling --skip_tools dnascope_filter --outdir results
tags:
- germline
- sentieon/dnascope_skip_filter
@@ -32,18 +32,13 @@
- path: results/sentieon_dnascope
should_exist: false
- path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt
- md5sum: e82e90c7d508a135b5a8a7cd6933452e
- path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt
- md5sum: 3a2030e5e8af7bc12720c3a5592bf921
- path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt
- md5sum: 615c5c5019d88045a9ff5bbe6e63d270
- path: results/reports/mosdepth/test/test.recal.regions.bed.gz
- md5sum: 9f1ea20e7461db948ba21f70c4d1b3ba
- path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi
- md5sum: 5c00a1d457c387d6e71848a6d897e309
- path: results/reports/samtools/test/test.recal.cram.stats
- name: Run variant calling on germline sample with sentieon dnascope without intervals and skip filter
- command: nextflow run main.nf -profile test_cache,targeted,software_license --sentieon_extension --input ./tests/csv/3.0/mapped_single_bam.csv --tools sentieon_dnascope --step variant_calling --skip_tools dnascope_filter --no_intervals --outdir results
+ command: nextflow run main.nf -profile test,targeted,software_license --sentieon_extension --input ./tests/csv/3.0/mapped_single_bam.csv --tools sentieon_dnascope --step variant_calling --skip_tools dnascope_filter --no_intervals --outdir results
tags:
- germline
- sentieon/dnascope_skip_filter
@@ -83,11 +78,7 @@
- path: results/sentieon_dnascope
should_exist: false
- path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt
- md5sum: e82e90c7d508a135b5a8a7cd6933452e
- path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt
- md5sum: 4f0d231060cbde4efdd673863bd2fb59
- path: results/reports/mosdepth/test/test.recal.per-base.bed.gz
- md5sum: bc1df47d46f818fee5275975925d769a
- path: results/reports/mosdepth/test/test.recal.per-base.bed.gz.csi
- md5sum: 9e649ac749ff6c6073bef5ab63e8aaa4
- path: results/reports/samtools/test/test.recal.cram.stats
diff --git a/tests/test_sentieon_haplotyper.yml b/tests/test_sentieon_haplotyper.yml
index b5f403710b..201d07a5be 100644
--- a/tests/test_sentieon_haplotyper.yml
+++ b/tests/test_sentieon_haplotyper.yml
@@ -1,5 +1,5 @@
- name: Run variant calling on germline sample with sentieons haplotyper
- command: nextflow run main.nf -profile test_cache,software_license,targeted --sentieon_extension --input ./tests/csv/3.0/mapped_single_bam.csv --tools sentieon_haplotyper --step variant_calling --outdir results
+ command: nextflow run main.nf -profile test,software_license,targeted --sentieon_extension --input ./tests/csv/3.0/mapped_single_bam.csv --tools sentieon_haplotyper --step variant_calling --outdir results
tags:
- germline
- sentieon/haplotyper
@@ -34,17 +34,13 @@
- path: results/haplotyper
should_exist: false
- path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt
- md5sum: e82e90c7d508a135b5a8a7cd6933452e
- path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt
- md5sum: 3a2030e5e8af7bc12720c3a5592bf921
- path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt
- path: results/reports/mosdepth/test/test.recal.regions.bed.gz
- md5sum: 9f1ea20e7461db948ba21f70c4d1b3ba
- path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi
- md5sum: 5c00a1d457c387d6e71848a6d897e309
- path: results/reports/samtools/test/test.recal.cram.stats
- name: Run variant calling on germline sample with sentieons haplotyper without intervals
- command: nextflow run main.nf -profile test_cache,software_license,targeted --sentieon_extension --input ./tests/csv/3.0/mapped_single_bam.csv --tools sentieon_haplotyper --step variant_calling --no_intervals --outdir results
+ command: nextflow run main.nf -profile test,software_license,targeted --sentieon_extension --input ./tests/csv/3.0/mapped_single_bam.csv --tools sentieon_haplotyper --step variant_calling --no_intervals --outdir results
tags:
- germline
- sentieon/haplotyper
@@ -86,15 +82,12 @@
- path: results/sentieon_haplotyper
should_exist: false
- path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt
- md5sum: e82e90c7d508a135b5a8a7cd6933452e
- path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt
- path: results/reports/mosdepth/test/test.recal.per-base.bed.gz
- md5sum: bc1df47d46f818fee5275975925d769a
- path: results/reports/mosdepth/test/test.recal.per-base.bed.gz.csi
- md5sum: 9e649ac749ff6c6073bef5ab63e8aaa4
- path: results/reports/samtools/test/test.recal.cram.stats
- name: Run variant calling on germline sample with sentieons haplotyper output gvcf
- command: nextflow run main.nf -profile test_cache,software_license,targeted --sentieon_extension --input ./tests/csv/3.0/mapped_single_bam.csv --tools sentieon_haplotyper --step variant_calling --outdir results --sentieon_haplotyper_emit_mode gvcf
+ command: nextflow run main.nf -profile test,software_license,targeted --sentieon_extension --input ./tests/csv/3.0/mapped_single_bam.csv --tools sentieon_haplotyper --step variant_calling --outdir results --sentieon_haplotyper_emit_mode gvcf
tags:
- germline
- sentieon/haplotyper
@@ -132,17 +125,13 @@
- path: results/haplotyper
should_exist: false
- path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt
- md5sum: e82e90c7d508a135b5a8a7cd6933452e
- path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt
- md5sum: 3a2030e5e8af7bc12720c3a5592bf921
- path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt
- path: results/reports/mosdepth/test/test.recal.regions.bed.gz
- md5sum: 9f1ea20e7461db948ba21f70c4d1b3ba
- path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi
- md5sum: 5c00a1d457c387d6e71848a6d897e309
- path: results/reports/samtools/test/test.recal.cram.stats
- name: Run variant calling on germline sample with sentieons haplotyper output both gvcf and vcf
- command: nextflow run main.nf -profile test_cache,software_license,targeted --sentieon_extension --input ./tests/csv/3.0/mapped_single_bam.csv --tools sentieon_haplotyper --step variant_calling --outdir results --sentieon_haplotyper_emit_mode variant,gvcf
+ command: nextflow run main.nf -profile test,software_license,targeted --sentieon_extension --input ./tests/csv/3.0/mapped_single_bam.csv --tools sentieon_haplotyper --step variant_calling --outdir results --sentieon_haplotyper_emit_mode variant,gvcf
tags:
- germline
- sentieon/haplotyper
@@ -172,17 +161,13 @@
- path: results/haplotyper
should_exist: false
- path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt
- md5sum: e82e90c7d508a135b5a8a7cd6933452e
- path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt
- md5sum: 3a2030e5e8af7bc12720c3a5592bf921
- path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt
- path: results/reports/mosdepth/test/test.recal.regions.bed.gz
- md5sum: 9f1ea20e7461db948ba21f70c4d1b3ba
- path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi
- md5sum: 5c00a1d457c387d6e71848a6d897e309
- path: results/reports/samtools/test/test.recal.cram.stats
- name: Run variant calling on germline sample with sentieons haplotyper and gatk haplotypecaller
- command: nextflow run main.nf -profile test_cache,software_license,targeted --sentieon_extension --input ./tests/csv/3.0/mapped_single_bam.csv --tools haplotypecaller,sentieon_haplotyper --step variant_calling --outdir results
+ command: nextflow run main.nf -profile test,software_license,targeted --sentieon_extension --input ./tests/csv/3.0/mapped_single_bam.csv --tools haplotypecaller,sentieon_haplotyper --step variant_calling --outdir results
tags:
- germline
- sentieon/haplotyper
@@ -225,12 +210,8 @@
- path: results/haplotyper
should_exist: false
- path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt
- md5sum: e82e90c7d508a135b5a8a7cd6933452e
- path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt
- md5sum: 3a2030e5e8af7bc12720c3a5592bf921
- path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt
- path: results/reports/mosdepth/test/test.recal.regions.bed.gz
- md5sum: 9f1ea20e7461db948ba21f70c4d1b3ba
- path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi
- md5sum: 5c00a1d457c387d6e71848a6d897e309
- path: results/reports/samtools/test/test.recal.cram.stats
diff --git a/tests/test_sentieon_haplotyper_joint_germline.yml b/tests/test_sentieon_haplotyper_joint_germline.yml
index 9469559f88..7dfa2d5d1d 100644
--- a/tests/test_sentieon_haplotyper_joint_germline.yml
+++ b/tests/test_sentieon_haplotyper_joint_germline.yml
@@ -1,5 +1,5 @@
- name: Run joint germline variant calling with sentieon haplotyper
- command: nextflow run main.nf -profile test_cache,software_license,targeted --sentieon_extension --input ./tests/csv/3.0/mapped_joint_bam.csv --tools sentieon_haplotyper --step variant_calling --joint_germline --outdir results --sentieon_haplotyper_emit_mode gvcf
+ command: nextflow run main.nf -profile test,software_license,targeted --sentieon_extension --input ./tests/csv/3.0/mapped_joint_bam.csv --tools sentieon_haplotyper --step variant_calling --joint_germline --outdir results --sentieon_haplotyper_emit_mode gvcf
tags:
- germline
- sentieon/haplotyper_joint_germline
@@ -27,29 +27,19 @@
- path: results/haplotyper
should_exist: false
- path: results/reports/mosdepth/testN/testN.recal.mosdepth.global.dist.txt
- md5sum: e82e90c7d508a135b5a8a7cd6933452e
- path: results/reports/mosdepth/testN/testN.recal.mosdepth.region.dist.txt
- md5sum: 3a2030e5e8af7bc12720c3a5592bf921
- path: results/reports/mosdepth/testN/testN.recal.mosdepth.summary.txt
- md5sum: 615c5c5019d88045a9ff5bbe6e63d270
- path: results/reports/mosdepth/testN/testN.recal.regions.bed.gz
- md5sum: 9f1ea20e7461db948ba21f70c4d1b3ba
- path: results/reports/mosdepth/testN/testN.recal.regions.bed.gz.csi
- md5sum: 5c00a1d457c387d6e71848a6d897e309
- path: results/reports/samtools/testN/testN.recal.cram.stats
- path: results/reports/mosdepth/testT/testT.recal.mosdepth.global.dist.txt
- md5sum: ba97ed85645f77da6f3adad138b3cdb4
- path: results/reports/mosdepth/testT/testT.recal.mosdepth.region.dist.txt
- md5sum: a7eb835371dd0aaf347ccca7ebe1eb3b
- path: results/reports/mosdepth/testT/testT.recal.mosdepth.summary.txt
- md5sum: a937108cbf24c1430b79c861234ce22b
- path: results/reports/mosdepth/testT/testT.recal.regions.bed.gz
- md5sum: d2b579a74bf8d858f82869f073056252
- path: results/reports/mosdepth/testT/testT.recal.regions.bed.gz.csi
- md5sum: 5c00a1d457c387d6e71848a6d897e309
- path: results/reports/samtools/testT/testT.recal.cram.stats
- name: Run joint germline variant calling with sentieon haplotyper all intervals at once
- command: nextflow run main.nf -profile test_cache,software_license,targeted --sentieon_extension --input ./tests/csv/3.0/mapped_joint_bam.csv --tools sentieon_haplotyper --step variant_calling --joint_germline --outdir results --sentieon_haplotyper_emit_mode gvcf --nucleotides_per_second 100
+ command: nextflow run main.nf -profile test,software_license,targeted --sentieon_extension --input ./tests/csv/3.0/mapped_joint_bam.csv --tools sentieon_haplotyper --step variant_calling --joint_germline --outdir results --sentieon_haplotyper_emit_mode gvcf --nucleotides_per_second 100
tags:
- germline
- sentieon/haplotyper_joint_germline
@@ -75,29 +65,19 @@
- path: results/haplotyper
should_exist: false
- path: results/reports/mosdepth/testN/testN.recal.mosdepth.global.dist.txt
- md5sum: e82e90c7d508a135b5a8a7cd6933452e
- path: results/reports/mosdepth/testN/testN.recal.mosdepth.region.dist.txt
- md5sum: 3a2030e5e8af7bc12720c3a5592bf921
- path: results/reports/mosdepth/testN/testN.recal.mosdepth.summary.txt
- md5sum: 615c5c5019d88045a9ff5bbe6e63d270
- path: results/reports/mosdepth/testN/testN.recal.regions.bed.gz
- md5sum: 9f1ea20e7461db948ba21f70c4d1b3ba
- path: results/reports/mosdepth/testN/testN.recal.regions.bed.gz.csi
- md5sum: 5c00a1d457c387d6e71848a6d897e309
- path: results/reports/samtools/testN/testN.recal.cram.stats
- path: results/reports/mosdepth/testT/testT.recal.mosdepth.global.dist.txt
- md5sum: ba97ed85645f77da6f3adad138b3cdb4
- path: results/reports/mosdepth/testT/testT.recal.mosdepth.region.dist.txt
- md5sum: a7eb835371dd0aaf347ccca7ebe1eb3b
- path: results/reports/mosdepth/testT/testT.recal.mosdepth.summary.txt
- md5sum: a937108cbf24c1430b79c861234ce22b
- path: results/reports/mosdepth/testT/testT.recal.regions.bed.gz
- md5sum: d2b579a74bf8d858f82869f073056252
- path: results/reports/mosdepth/testT/testT.recal.regions.bed.gz.csi
- md5sum: 5c00a1d457c387d6e71848a6d897e309
- path: results/reports/samtools/testT/testT.recal.cram.stats
- name: Run joint germline variant calling with sentieon haplotyper with stub for VQSR
- command: nextflow run main.nf -profile test_cache,software_license,tools_germline --sentieon_extension --input ./tests/csv/3.0/mapped_joint_bam.csv --tools sentieon_haplotyper --step variant_calling --joint_germline --outdir results --sentieon_haplotyper_emit_mode gvcf -stub-run
+ command: nextflow run main.nf -profile test,software_license,tools_germline --sentieon_extension --input ./tests/csv/3.0/mapped_joint_bam.csv --tools sentieon_haplotyper --step variant_calling --joint_germline --outdir results --sentieon_haplotyper_emit_mode gvcf -stub-run
tags:
- germline
- sentieon/haplotyper_joint_germline
@@ -123,24 +103,14 @@
- path: results/haplotyper
should_exist: false
- path: results/reports/mosdepth/testN/testN.recal.global.dist.txt
- md5sum: d41d8cd98f00b204e9800998ecf8427e
- path: results/reports/mosdepth/testN/testN.recal.region.dist.txt
- md5sum: d41d8cd98f00b204e9800998ecf8427e
- path: results/reports/mosdepth/testN/testN.recal.summary.txt
- md5sum: d41d8cd98f00b204e9800998ecf8427e
- path: results/reports/mosdepth/testN/testN.recal.regions.bed.gz
- md5sum: 1a60c330fb42841e8dcf3cd507a70bfc
- path: results/reports/mosdepth/testN/testN.recal.regions.bed.gz.csi
- md5sum: d41d8cd98f00b204e9800998ecf8427e
- path: results/reports/samtools/testN/testN.recal.cram.stats
- path: results/reports/mosdepth/testT/testT.recal.global.dist.txt
- md5sum: d41d8cd98f00b204e9800998ecf8427e
- path: results/reports/mosdepth/testT/testT.recal.region.dist.txt
- md5sum: d41d8cd98f00b204e9800998ecf8427e
- path: results/reports/mosdepth/testT/testT.recal.summary.txt
- md5sum: d41d8cd98f00b204e9800998ecf8427e
- path: results/reports/mosdepth/testT/testT.recal.regions.bed.gz
- md5sum: 1a60c330fb42841e8dcf3cd507a70bfc
- path: results/reports/mosdepth/testT/testT.recal.regions.bed.gz.csi
- md5sum: d41d8cd98f00b204e9800998ecf8427e
- path: results/reports/samtools/testT/testT.recal.cram.stats
diff --git a/tests/test_sentieon_haplotyper_skip_filter.yml b/tests/test_sentieon_haplotyper_skip_filter.yml
index f599260b5f..7328e9a4ec 100644
--- a/tests/test_sentieon_haplotyper_skip_filter.yml
+++ b/tests/test_sentieon_haplotyper_skip_filter.yml
@@ -1,5 +1,5 @@
- name: Run variant calling on germline sample with sentieon haplotyper and skip filter
- command: nextflow run main.nf -profile test_cache,software_license,targeted --sentieon_extension --input ./tests/csv/3.0/mapped_single_bam.csv --tools sentieon_haplotyper --step variant_calling --skip_tools haplotyper_filter --outdir results
+ command: nextflow run main.nf -profile test,software_license,targeted --sentieon_extension --input ./tests/csv/3.0/mapped_single_bam.csv --tools sentieon_haplotyper --step variant_calling --skip_tools haplotyper_filter --outdir results
tags:
- germline
- sentieon/haplotyper_skip_filter
@@ -34,15 +34,12 @@
- path: results/sentieon_haplotyper
should_exist: false
- path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt
- md5sum: e82e90c7d508a135b5a8a7cd6933452e
- path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt
- path: results/reports/mosdepth/test/test.recal.per-base.bed.gz
- md5sum: bc1df47d46f818fee5275975925d769a
- path: results/reports/mosdepth/test/test.recal.per-base.bed.gz.csi
- md5sum: 9e649ac749ff6c6073bef5ab63e8aaa4
- path: results/reports/samtools/test/test.recal.cram.stats
- name: Run variant calling on germline sample with sentieon haplotyper without intervals and skip filter
- command: nextflow run main.nf -profile test_cache,software_license,targeted --sentieon_extension --input ./tests/csv/3.0/mapped_single_bam.csv --tools sentieon_haplotyper --step variant_calling --skip_tools haplotyper_filter --no_intervals --outdir results
+ command: nextflow run main.nf -profile test,software_license,targeted --sentieon_extension --input ./tests/csv/3.0/mapped_single_bam.csv --tools sentieon_haplotyper --step variant_calling --skip_tools haplotyper_filter --no_intervals --outdir results
tags:
- germline
- sentieon/haplotyper_skip_filter
@@ -84,10 +81,7 @@
- path: results/sentieon_haplotyper
should_exist: false
- path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt
- md5sum: e82e90c7d508a135b5a8a7cd6933452e
- path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt
- path: results/reports/mosdepth/test/test.recal.per-base.bed.gz
- md5sum: bc1df47d46f818fee5275975925d769a
- path: results/reports/mosdepth/test/test.recal.per-base.bed.gz.csi
- md5sum: 9e649ac749ff6c6073bef5ab63e8aaa4
- path: results/reports/samtools/test/test.recal.cram.stats
diff --git a/tests/test_skip_all_qc.yml b/tests/test_skip_all_qc.yml
index 9e2ef2ceb1..24938562c2 100644
--- a/tests/test_skip_all_qc.yml
+++ b/tests/test_skip_all_qc.yml
@@ -1,5 +1,5 @@
- name: Run default pipeline with skipping all QC steps
- command: nextflow run main.nf -profile test_cache --skip_tools fastqc,markduplicates_report,mosdepth,multiqc,samtools --outdir results
+ command: nextflow run main.nf -profile test --skip_tools fastqc,markduplicates_report,mosdepth,multiqc,samtools --outdir results
tags:
- default_extended
- preprocessing
diff --git a/tests/test_skip_markduplicates.yml b/tests/test_skip_markduplicates.yml
index d683b6952d..93718954c8 100644
--- a/tests/test_skip_markduplicates.yml
+++ b/tests/test_skip_markduplicates.yml
@@ -1,5 +1,5 @@
- name: Run default pipeline with skipping Markduplicates
- command: nextflow run main.nf -profile test_cache,skip_markduplicates --outdir results
+ command: nextflow run main.nf -profile test,skip_markduplicates --outdir results
tags:
- default_extended
- preprocessing
@@ -22,25 +22,15 @@
# binary changes md5sums on reruns
- path: results/reports/fastqc/test-test_L1
- path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt
- md5sum: 3ab32cc98996e0f12b8088b99dd1e2d1
- path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt
- md5sum: 1653d9aa161a78d8574269083f7d92f1
- path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt
- md5sum: b8874be5d830a2d03d42bccad7c996d3
- path: results/reports/mosdepth/test/test.recal.regions.bed.gz
- md5sum: 67ac075b077723fb1cce4b026dcdf0af
- path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi
- md5sum: 3230b6808c22d4907d18910f2dc2daf2
- path: results/reports/mosdepth/test/test.sorted.mosdepth.global.dist.txt
- md5sum: 3ab32cc98996e0f12b8088b99dd1e2d1
- path: results/reports/mosdepth/test/test.sorted.mosdepth.region.dist.txt
- md5sum: 1653d9aa161a78d8574269083f7d92f1
- path: results/reports/mosdepth/test/test.sorted.mosdepth.summary.txt
- md5sum: b8874be5d830a2d03d42bccad7c996d3
- path: results/reports/mosdepth/test/test.sorted.regions.bed.gz
- md5sum: 67ac075b077723fb1cce4b026dcdf0af
- path: results/reports/mosdepth/test/test.sorted.regions.bed.gz.csi
- md5sum: 3230b6808c22d4907d18910f2dc2daf2
- path: results/reports/samtools/test/test.recal.cram.stats
# conda changes md5sums for test
- path: results/reports/samtools/test/test.sorted.cram.stats
@@ -54,7 +44,7 @@
- path: results/preprocessing/mapped/test/test.sorted.bam
should_exist: false
- name: Run default pipeline with skipping Markduplicates with save_mapped
- command: nextflow run main.nf -profile test_cache,skip_markduplicates --save_mapped --outdir results
+ command: nextflow run main.nf -profile test,skip_markduplicates --save_mapped --outdir results
tags:
- default_extended
- preprocessing
@@ -78,25 +68,15 @@
# binary changes md5sums on reruns
- path: results/reports/fastqc/test-test_L1
- path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt
- md5sum: 3ab32cc98996e0f12b8088b99dd1e2d1
- path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt
- md5sum: 1653d9aa161a78d8574269083f7d92f1
- path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt
- md5sum: b8874be5d830a2d03d42bccad7c996d3
- path: results/reports/mosdepth/test/test.recal.regions.bed.gz
- md5sum: 67ac075b077723fb1cce4b026dcdf0af
- path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi
- md5sum: 3230b6808c22d4907d18910f2dc2daf2
- path: results/reports/mosdepth/test/test.sorted.mosdepth.global.dist.txt
- md5sum: 3ab32cc98996e0f12b8088b99dd1e2d1
- path: results/reports/mosdepth/test/test.sorted.mosdepth.region.dist.txt
- md5sum: 1653d9aa161a78d8574269083f7d92f1
- path: results/reports/mosdepth/test/test.sorted.mosdepth.summary.txt
- md5sum: b8874be5d830a2d03d42bccad7c996d3
- path: results/reports/mosdepth/test/test.sorted.regions.bed.gz
- md5sum: 67ac075b077723fb1cce4b026dcdf0af
- path: results/reports/mosdepth/test/test.sorted.regions.bed.gz.csi
- md5sum: 3230b6808c22d4907d18910f2dc2daf2
- path: results/reports/samtools/test/test.recal.cram.stats
# conda changes md5sums for test
- path: results/reports/samtools/test/test.sorted.cram.stats
@@ -108,7 +88,7 @@
- path: results/preprocessing/mapped/test/test.bam
should_exist: false
- name: Run default pipeline with skipping Markduplicates with save_mapped & save_output_as_bam
- command: nextflow run main.nf -profile test_cache,skip_markduplicates --save_mapped --save_output_as_bam --outdir results
+ command: nextflow run main.nf -profile test,skip_markduplicates --save_mapped --save_output_as_bam --outdir results
tags:
- default_extended
- preprocessing
@@ -132,25 +112,15 @@
# binary changes md5sums on reruns
- path: results/reports/fastqc/test-test_L1
- path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt
- md5sum: 3ab32cc98996e0f12b8088b99dd1e2d1
- path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt
- md5sum: 1653d9aa161a78d8574269083f7d92f1
- path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt
- md5sum: b8874be5d830a2d03d42bccad7c996d3
- path: results/reports/mosdepth/test/test.recal.regions.bed.gz
- md5sum: 67ac075b077723fb1cce4b026dcdf0af
- path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi
- md5sum: 3230b6808c22d4907d18910f2dc2daf2
- path: results/reports/mosdepth/test/test.sorted.mosdepth.global.dist.txt
- md5sum: 3ab32cc98996e0f12b8088b99dd1e2d1
- path: results/reports/mosdepth/test/test.sorted.mosdepth.region.dist.txt
- md5sum: 1653d9aa161a78d8574269083f7d92f1
- path: results/reports/mosdepth/test/test.sorted.mosdepth.summary.txt
- md5sum: b8874be5d830a2d03d42bccad7c996d3
- path: results/reports/mosdepth/test/test.sorted.regions.bed.gz
- md5sum: 67ac075b077723fb1cce4b026dcdf0af
- path: results/reports/mosdepth/test/test.sorted.regions.bed.gz.csi
- md5sum: 3230b6808c22d4907d18910f2dc2daf2
- path: results/reports/samtools/test/test.recal.cram.stats
# conda changes md5sums for test
- path: results/reports/samtools/test/test.sorted.cram.stats
diff --git a/tests/test_strelka.yml b/tests/test_strelka.yml
index 766d9e18c7..b2b25672a2 100644
--- a/tests/test_strelka.yml
+++ b/tests/test_strelka.yml
@@ -1,5 +1,5 @@
- name: Skip variant calling on matched normal
- command: nextflow run main.nf -profile test_cache,variantcalling_channels --tools strelka --only_paired_variant_calling --outdir results
+ command: nextflow run main.nf -profile test,variantcalling_channels --tools strelka --only_paired_variant_calling --outdir results
tags:
- somatic
- strelka
@@ -77,53 +77,33 @@
- path: results/variant_calling/strelka/sample3/sample3.strelka.genome.vcf.gz.tbi
should_exist: false
- path: results/reports/mosdepth/sample1/sample1.recal.mosdepth.global.dist.txt
- md5sum: 69e29702ef01fd8f6c7a5468fc35a16a
- path: results/reports/mosdepth/sample1/sample1.recal.mosdepth.region.dist.txt
- md5sum: 6ec49cd7d510c2eb3d9d90fdb79b783a
- path: results/reports/mosdepth/sample1/sample1.recal.mosdepth.summary.txt
- md5sum: 103098d0bf76ed82d2b87d5f242b099a
- path: results/reports/mosdepth/sample1/sample1.recal.regions.bed.gz
- md5sum: b5888cf7395c57d39879a5faa6159eb3
- path: results/reports/mosdepth/sample1/sample1.recal.regions.bed.gz.csi
- md5sum: 9cb0ad7039a3b703d16ca7d5b835c0ee
- path: results/reports/samtools/sample1/sample1.recal.cram.stats
- path: results/reports/mosdepth/sample2/sample2.recal.mosdepth.global.dist.txt
- md5sum: f2dcd00a64947c49e8e4b93c2f4fbf27
- path: results/reports/mosdepth/sample2/sample2.recal.mosdepth.region.dist.txt
- md5sum: 39005ffaac22871ffaaf19656fe69c5b
- path: results/reports/mosdepth/sample2/sample2.recal.mosdepth.summary.txt
- md5sum: 68d4b98f17361fddf73052ead34fa370
- path: results/reports/mosdepth/sample2/sample2.recal.regions.bed.gz
- md5sum: 2819e995eafded35f53328c4ec19ba58
- path: results/reports/mosdepth/sample2/sample2.recal.regions.bed.gz.csi
- md5sum: 393c2749068304d8545b501b9d4658e4
- path: results/reports/samtools/sample2/sample2.recal.cram.stats
- path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.global.dist.txt
- md5sum: 69e29702ef01fd8f6c7a5468fc35a16a
- path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.region.dist.txt
- md5sum: 6ec49cd7d510c2eb3d9d90fdb79b783a
- path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.summary.txt
- md5sum: 103098d0bf76ed82d2b87d5f242b099a
- path: results/reports/mosdepth/sample3/sample3.recal.regions.bed.gz
- md5sum: b5888cf7395c57d39879a5faa6159eb3
- path: results/reports/mosdepth/sample3/sample3.recal.regions.bed.gz.csi
- md5sum: 9cb0ad7039a3b703d16ca7d5b835c0ee
- path: results/reports/samtools/sample3/sample3.recal.cram.stats
# conda changes md5sums for test
- path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.global.dist.txt
- md5sum: f2dcd00a64947c49e8e4b93c2f4fbf27
- path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.region.dist.txt
- md5sum: 39005ffaac22871ffaaf19656fe69c5b
- path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.summary.txt
- md5sum: 68d4b98f17361fddf73052ead34fa370
- path: results/reports/mosdepth/sample4/sample4.recal.regions.bed.gz
- md5sum: 2819e995eafded35f53328c4ec19ba58
- path: results/reports/mosdepth/sample4/sample4.recal.regions.bed.gz.csi
- md5sum: 393c2749068304d8545b501b9d4658e4
- path: results/reports/samtools/sample4/sample4.recal.cram.stats
# conda changes md5sums for test
- name: Run variant calling on germline sample with strelka
- command: nextflow run main.nf -profile test_cache,tools_germline --tools strelka --outdir results
+ command: nextflow run main.nf -profile test,tools_germline --tools strelka --outdir results
tags:
- germline
- strelka
@@ -151,18 +131,13 @@
- path: results/strelka
should_exist: false
- path: results/reports/mosdepth/sample1/sample1.recal.mosdepth.global.dist.txt
- md5sum: 69e29702ef01fd8f6c7a5468fc35a16a
- path: results/reports/mosdepth/sample1/sample1.recal.mosdepth.region.dist.txt
- md5sum: 6ec49cd7d510c2eb3d9d90fdb79b783a
- path: results/reports/mosdepth/sample1/sample1.recal.mosdepth.summary.txt
- md5sum: 103098d0bf76ed82d2b87d5f242b099a
- path: results/reports/mosdepth/sample1/sample1.recal.regions.bed.gz
- md5sum: b5888cf7395c57d39879a5faa6159eb3
- path: results/reports/mosdepth/sample1/sample1.recal.regions.bed.gz.csi
- md5sum: 9cb0ad7039a3b703d16ca7d5b835c0ee
- path: results/reports/samtools/sample1/sample1.recal.cram.stats
- name: Run variant calling on germline sample with strelka without intervals
- command: nextflow run main.nf -profile test_cache,tools_germline --tools strelka --no_intervals --outdir results
+ command: nextflow run main.nf -profile test,tools_germline --tools strelka --no_intervals --outdir results
tags:
- germline
- strelka
@@ -197,16 +172,12 @@
- path: results/strelka
should_exist: false
- path: results/reports/mosdepth/sample1/sample1.recal.mosdepth.global.dist.txt
- md5sum: 69e29702ef01fd8f6c7a5468fc35a16a
- path: results/reports/mosdepth/sample1/sample1.recal.mosdepth.summary.txt
- md5sum: d2775eb102acc5950f7f53883dcb503d
- path: results/reports/mosdepth/sample1/sample1.recal.per-base.bed.gz
- md5sum: 54431f155c9538809e8caf99d1a75ec7
- path: results/reports/mosdepth/sample1/sample1.recal.per-base.bed.gz.csi
- md5sum: c67dcd711b096eb42f43784d5eadbc0d
- path: results/reports/samtools/sample1/sample1.recal.cram.stats
- name: Run variant calling on tumor only sample with strelka
- command: nextflow run main.nf -profile test_cache,tools_tumoronly --tools strelka --outdir results
+ command: nextflow run main.nf -profile test,tools_tumoronly --tools strelka --outdir results
tags:
- strelka
- tumor_only
@@ -234,18 +205,13 @@
- path: results/strelka
should_exist: false
- path: results/reports/mosdepth/sample2/sample2.recal.mosdepth.global.dist.txt
- md5sum: f2dcd00a64947c49e8e4b93c2f4fbf27
- path: results/reports/mosdepth/sample2/sample2.recal.mosdepth.region.dist.txt
- md5sum: 39005ffaac22871ffaaf19656fe69c5b
- path: results/reports/mosdepth/sample2/sample2.recal.mosdepth.summary.txt
- md5sum: 68d4b98f17361fddf73052ead34fa370
- path: results/reports/mosdepth/sample2/sample2.recal.regions.bed.gz
- md5sum: 2819e995eafded35f53328c4ec19ba58
- path: results/reports/mosdepth/sample2/sample2.recal.regions.bed.gz.csi
- md5sum: 393c2749068304d8545b501b9d4658e4
- path: results/reports/samtools/sample2/sample2.recal.cram.stats
- name: Run variant calling on tumor only sample with strelka without intervals
- command: nextflow run main.nf -profile test_cache,tools_tumoronly --tools strelka --no_intervals --outdir results
+ command: nextflow run main.nf -profile test,tools_tumoronly --tools strelka --no_intervals --outdir results
tags:
- no_intervals
- strelka
@@ -280,16 +246,12 @@
- path: results/strelka
should_exist: false
- path: results/reports/mosdepth/sample2/sample2.recal.mosdepth.global.dist.txt
- md5sum: f2dcd00a64947c49e8e4b93c2f4fbf27
- path: results/reports/mosdepth/sample2/sample2.recal.mosdepth.summary.txt
- md5sum: 0a7300e56eda6fba7c7564f00aa000f0
- path: results/reports/mosdepth/sample2/sample2.recal.per-base.bed.gz
- md5sum: 3de4a9f4da2f2b4909ef192452a8d211
- path: results/reports/mosdepth/sample2/sample2.recal.per-base.bed.gz.csi
- md5sum: cfb07b0ba46e8468b4342edb243536f3
- path: results/reports/samtools/sample2/sample2.recal.cram.stats
- name: Run variant calling on somatic sample with strelka
- command: nextflow run main.nf -profile test_cache,tools_somatic --tools strelka --outdir results
+ command: nextflow run main.nf -profile test,tools_somatic --tools strelka --outdir results
tags:
- somatic
- strelka
@@ -341,31 +303,21 @@
- path: results/strelka
should_exist: false
- path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.global.dist.txt
- md5sum: 69e29702ef01fd8f6c7a5468fc35a16a
- path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.region.dist.txt
- md5sum: 6ec49cd7d510c2eb3d9d90fdb79b783a
- path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.summary.txt
- md5sum: 103098d0bf76ed82d2b87d5f242b099a
- path: results/reports/mosdepth/sample3/sample3.recal.regions.bed.gz
- md5sum: b5888cf7395c57d39879a5faa6159eb3
- path: results/reports/mosdepth/sample3/sample3.recal.regions.bed.gz.csi
- md5sum: 9cb0ad7039a3b703d16ca7d5b835c0ee
- path: results/reports/samtools/sample3/sample3.recal.cram.stats
# conda changes md5sums for test
- path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.global.dist.txt
- md5sum: f2dcd00a64947c49e8e4b93c2f4fbf27
- path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.region.dist.txt
- md5sum: 39005ffaac22871ffaaf19656fe69c5b
- path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.summary.txt
- md5sum: 68d4b98f17361fddf73052ead34fa370
- path: results/reports/mosdepth/sample4/sample4.recal.regions.bed.gz
- md5sum: 2819e995eafded35f53328c4ec19ba58
- path: results/reports/mosdepth/sample4/sample4.recal.regions.bed.gz.csi
- md5sum: 393c2749068304d8545b501b9d4658e4
- path: results/reports/samtools/sample4/sample4.recal.cram.stats
# conda changes md5sums for test
- name: Run variant calling on somatic sample with strelka without intervals
- command: nextflow run main.nf -profile test_cache,tools_somatic --tools strelka --no_intervals --outdir results
+ command: nextflow run main.nf -profile test,tools_somatic --tools strelka --no_intervals --outdir results
tags:
- no_intervals
- somatic
@@ -424,22 +376,14 @@
- path: results/strelka
should_exist: false
- path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.global.dist.txt
- md5sum: 69e29702ef01fd8f6c7a5468fc35a16a
- path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.summary.txt
- md5sum: d2775eb102acc5950f7f53883dcb503d
- path: results/reports/mosdepth/sample3/sample3.recal.per-base.bed.gz
- md5sum: 54431f155c9538809e8caf99d1a75ec7
- path: results/reports/mosdepth/sample3/sample3.recal.per-base.bed.gz.csi
- md5sum: c67dcd711b096eb42f43784d5eadbc0d
- path: results/reports/samtools/sample3/sample3.recal.cram.stats
# conda changes md5sums for test
- path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.global.dist.txt
- md5sum: f2dcd00a64947c49e8e4b93c2f4fbf27
- path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.summary.txt
- md5sum: 0a7300e56eda6fba7c7564f00aa000f0
- path: results/reports/mosdepth/sample4/sample4.recal.per-base.bed.gz
- md5sum: 3de4a9f4da2f2b4909ef192452a8d211
- path: results/reports/mosdepth/sample4/sample4.recal.per-base.bed.gz.csi
- md5sum: cfb07b0ba46e8468b4342edb243536f3
- path: results/reports/samtools/sample4/sample4.recal.cram.stats
# conda changes md5sums for test
diff --git a/tests/test_strelka_bp.yml b/tests/test_strelka_bp.yml
index b813f648d8..f5954de37c 100644
--- a/tests/test_strelka_bp.yml
+++ b/tests/test_strelka_bp.yml
@@ -1,5 +1,5 @@
- name: Run variant calling on somatic sample with Strelka BP
- command: nextflow run main.nf -profile test_cache,tools_somatic --tools strelka,manta --outdir results
+ command: nextflow run main.nf -profile test,tools_somatic --tools strelka,manta --outdir results
tags:
- somatic
- strelka_bp
@@ -89,31 +89,21 @@
- path: results/strelka
should_exist: false
- path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.global.dist.txt
- md5sum: 69e29702ef01fd8f6c7a5468fc35a16a
- path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.region.dist.txt
- md5sum: 6ec49cd7d510c2eb3d9d90fdb79b783a
- path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.summary.txt
- md5sum: 103098d0bf76ed82d2b87d5f242b099a
- path: results/reports/mosdepth/sample3/sample3.recal.regions.bed.gz
- md5sum: b5888cf7395c57d39879a5faa6159eb3
- path: results/reports/mosdepth/sample3/sample3.recal.regions.bed.gz.csi
- md5sum: 9cb0ad7039a3b703d16ca7d5b835c0ee
- path: results/reports/samtools/sample3/sample3.recal.cram.stats
# conda changes md5sums for test
- path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.global.dist.txt
- md5sum: f2dcd00a64947c49e8e4b93c2f4fbf27
- path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.region.dist.txt
- md5sum: 39005ffaac22871ffaaf19656fe69c5b
- path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.summary.txt
- md5sum: 68d4b98f17361fddf73052ead34fa370
- path: results/reports/mosdepth/sample4/sample4.recal.regions.bed.gz
- md5sum: 2819e995eafded35f53328c4ec19ba58
- path: results/reports/mosdepth/sample4/sample4.recal.regions.bed.gz.csi
- md5sum: 393c2749068304d8545b501b9d4658e4
- path: results/reports/samtools/sample4/sample4.recal.cram.stats
# conda changes md5sums for test
- name: Run variant calling on somatic sample with Strelka BP without intervals
- command: nextflow run main.nf -profile test_cache,tools_somatic --tools strelka,manta --no_intervals --outdir results
+ command: nextflow run main.nf -profile test,tools_somatic --tools strelka,manta --no_intervals --outdir results
tags:
- no_intervals
- somatic
@@ -210,22 +200,14 @@
- path: results/strelka
should_exist: false
- path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.global.dist.txt
- md5sum: 69e29702ef01fd8f6c7a5468fc35a16a
- path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.summary.txt
- md5sum: d2775eb102acc5950f7f53883dcb503d
- path: results/reports/mosdepth/sample3/sample3.recal.per-base.bed.gz
- md5sum: 54431f155c9538809e8caf99d1a75ec7
- path: results/reports/mosdepth/sample3/sample3.recal.per-base.bed.gz.csi
- md5sum: c67dcd711b096eb42f43784d5eadbc0d
- path: results/reports/samtools/sample3/sample3.recal.cram.stats
# conda changes md5sums for test
- path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.global.dist.txt
- md5sum: f2dcd00a64947c49e8e4b93c2f4fbf27
- path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.summary.txt
- md5sum: 0a7300e56eda6fba7c7564f00aa000f0
- path: results/reports/mosdepth/sample4/sample4.recal.per-base.bed.gz
- md5sum: 3de4a9f4da2f2b4909ef192452a8d211
- path: results/reports/mosdepth/sample4/sample4.recal.per-base.bed.gz.csi
- md5sum: cfb07b0ba46e8468b4342edb243536f3
- path: results/reports/samtools/sample4/sample4.recal.cram.stats
# conda changes md5sums for test
diff --git a/tests/test_tiddit.yml b/tests/test_tiddit.yml
index abac99f94b..7d397e08a4 100644
--- a/tests/test_tiddit.yml
+++ b/tests/test_tiddit.yml
@@ -1,5 +1,5 @@
- name: Run variant calling on somatic sample with tiddit
- command: nextflow run main.nf -profile test_cache,tools_somatic --tools tiddit --outdir results
+ command: nextflow run main.nf -profile test,tools_somatic --tools tiddit --outdir results
tags:
- tiddit
- somatic
@@ -45,31 +45,21 @@
- path: results/tiddit
should_exist: false
- path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.global.dist.txt
- md5sum: 69e29702ef01fd8f6c7a5468fc35a16a
- path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.region.dist.txt
- md5sum: 6ec49cd7d510c2eb3d9d90fdb79b783a
- path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.summary.txt
- md5sum: 103098d0bf76ed82d2b87d5f242b099a
- path: results/reports/mosdepth/sample3/sample3.recal.regions.bed.gz
- md5sum: b5888cf7395c57d39879a5faa6159eb3
- path: results/reports/mosdepth/sample3/sample3.recal.regions.bed.gz.csi
- md5sum: 9cb0ad7039a3b703d16ca7d5b835c0ee
- path: results/reports/samtools/sample3/sample3.recal.cram.stats
# conda changes md5sums for test
- path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.global.dist.txt
- md5sum: f2dcd00a64947c49e8e4b93c2f4fbf27
- path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.region.dist.txt
- md5sum: 39005ffaac22871ffaaf19656fe69c5b
- path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.summary.txt
- md5sum: 68d4b98f17361fddf73052ead34fa370
- path: results/reports/mosdepth/sample4/sample4.recal.regions.bed.gz
- md5sum: 2819e995eafded35f53328c4ec19ba58
- path: results/reports/mosdepth/sample4/sample4.recal.regions.bed.gz.csi
- md5sum: 393c2749068304d8545b501b9d4658e4
- path: results/reports/samtools/sample4/sample4.recal.cram.stats
# conda changes md5sums for test
- name: Run variant calling on germline sample with tiddit
- command: nextflow run main.nf -profile test_cache,tools_germline --tools tiddit --outdir results
+ command: nextflow run main.nf -profile test,tools_germline --tools tiddit --outdir results
tags:
- tiddit
- germline
@@ -95,18 +85,13 @@
- path: results/tiddit
should_exist: false
- path: results/reports/mosdepth/sample1/sample1.recal.mosdepth.global.dist.txt
- md5sum: 69e29702ef01fd8f6c7a5468fc35a16a
- path: results/reports/mosdepth/sample1/sample1.recal.mosdepth.region.dist.txt
- md5sum: 6ec49cd7d510c2eb3d9d90fdb79b783a
- path: results/reports/mosdepth/sample1/sample1.recal.mosdepth.summary.txt
- md5sum: 103098d0bf76ed82d2b87d5f242b099a
- path: results/reports/mosdepth/sample1/sample1.recal.regions.bed.gz
- md5sum: b5888cf7395c57d39879a5faa6159eb3
- path: results/reports/mosdepth/sample1/sample1.recal.regions.bed.gz.csi
- md5sum: 9cb0ad7039a3b703d16ca7d5b835c0ee
- path: results/reports/samtools/sample1/sample1.recal.cram.stats
- name: Run variant calling on tumor_only sample with tiddit
- command: nextflow run main.nf -profile test_cache,tools_tumoronly --tools tiddit --outdir results
+ command: nextflow run main.nf -profile test,tools_tumoronly --tools tiddit --outdir results
tags:
- tiddit
- tumor_only
@@ -132,13 +117,8 @@
- path: results/tiddit
should_exist: false
- path: results/reports/mosdepth/sample2/sample2.recal.mosdepth.global.dist.txt
- md5sum: f2dcd00a64947c49e8e4b93c2f4fbf27
- path: results/reports/mosdepth/sample2/sample2.recal.mosdepth.region.dist.txt
- md5sum: 39005ffaac22871ffaaf19656fe69c5b
- path: results/reports/mosdepth/sample2/sample2.recal.mosdepth.summary.txt
- md5sum: 68d4b98f17361fddf73052ead34fa370
- path: results/reports/mosdepth/sample2/sample2.recal.regions.bed.gz
- md5sum: 2819e995eafded35f53328c4ec19ba58
- path: results/reports/mosdepth/sample2/sample2.recal.regions.bed.gz.csi
- md5sum: 393c2749068304d8545b501b9d4658e4
- path: results/reports/samtools/sample2/sample2.recal.cram.stats
diff --git a/tests/test_tools_manually.yml b/tests/test_tools_manually.yml
index 8725ec6a64..fe1642b3c3 100644
--- a/tests/test_tools_manually.yml
+++ b/tests/test_tools_manually.yml
@@ -1,5 +1,5 @@
- name: Run variant calling on somatic samples with ascat
- command: nextflow run main.nf -profile test_cache,tools_somatic_ascat --outdir results
+ command: nextflow run main.nf -profile test,tools_somatic_ascat --outdir results
tags:
- ascat_manual
- manual
@@ -35,31 +35,21 @@
- path: results/variant_calling/ascat/sample4_vs_sample3/sample4_vs_sample3.tumour_normalLogR.txt
md5sum: 05418a7d814db11808172a4f57d040a1
- path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.global.dist.txt
- md5sum: 69e29702ef01fd8f6c7a5468fc35a16a
- path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.region.dist.txt
- md5sum: 6ec49cd7d510c2eb3d9d90fdb79b783a
- path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.summary.txt
- md5sum: 103098d0bf76ed82d2b87d5f242b099a
- path: results/reports/mosdepth/sample3/sample3.recal.regions.bed.gz
- md5sum: b5888cf7395c57d39879a5faa6159eb3
- path: results/reports/mosdepth/sample3/sample3.recal.regions.bed.gz.csi
- md5sum: 9cb0ad7039a3b703d16ca7d5b835c0ee
- path: results/reports/samtools/sample3/sample3.recal.cram.stats
# conda changes md5sums for test
- path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.global.dist.txt
- md5sum: f2dcd00a64947c49e8e4b93c2f4fbf27
- path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.region.dist.txt
- md5sum: 39005ffaac22871ffaaf19656fe69c5b
- path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.summary.txt
- md5sum: 68d4b98f17361fddf73052ead34fa370
- path: results/reports/mosdepth/sample4/sample4.recal.regions.bed.gz
- md5sum: 2819e995eafded35f53328c4ec19ba58
- path: results/reports/mosdepth/sample4/sample4.recal.regions.bed.gz.csi
- md5sum: 393c2749068304d8545b501b9d4658e4
- path: results/reports/samtools/sample4/sample4.recal.cram.stats
# conda changes md5sums for test
- name: Run variant calling on somatic sample with mutect2 without intervals
- command: nextflow run main.nf -profile test_cache,tools_somatic --tools mutect2 --no_intervals --outdir results
+ command: nextflow run main.nf -profile test,tools_somatic --tools mutect2 --no_intervals --outdir results
tags:
- mutect2_manual
- manual
@@ -107,27 +97,19 @@
- path: results/variant_calling/mutect2/sample4_vs_sample3/sample4_vs_sample3.mutect2.vcf.gz.tbi
# binary changes md5sums on reruns
- path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.global.dist.txt
- md5sum: 69e29702ef01fd8f6c7a5468fc35a16a
- path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.summary.txt
- md5sum: d2775eb102acc5950f7f53883dcb503d
- path: results/reports/mosdepth/sample3/sample3.recal.per-base.bed.gz
- md5sum: 54431f155c9538809e8caf99d1a75ec7
- path: results/reports/mosdepth/sample3/sample3.recal.per-base.bed.gz.csi
- md5sum: c67dcd711b096eb42f43784d5eadbc0d
- path: results/reports/samtools/sample3/sample3.recal.cram.stats
# conda changes md5sums for test
- path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.global.dist.txt
- md5sum: f2dcd00a64947c49e8e4b93c2f4fbf27
- path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.summary.txt
- md5sum: 0a7300e56eda6fba7c7564f00aa000f0
- path: results/reports/mosdepth/sample4/sample4.recal.per-base.bed.gz
- md5sum: 3de4a9f4da2f2b4909ef192452a8d211
- path: results/reports/mosdepth/sample4/sample4.recal.per-base.bed.gz.csi
- md5sum: cfb07b0ba46e8468b4342edb243536f3
- path: results/reports/samtools/sample4/sample4.recal.cram.stats
# conda changes md5sums for test
- name: Run variant calling on somatic sample with mutect2
- command: nextflow run main.nf -profile test_cache,tools_somatic --tools mutect2 --outdir results
+ command: nextflow run main.nf -profile test,tools_somatic --tools mutect2 --outdir results
tags:
- mutect2_manual
- manual
@@ -168,31 +150,21 @@
- path: results/variant_calling/mutect2/sample4_vs_sample3/sample4_vs_sample3.mutect2.vcf.gz.tbi
# binary changes md5sums on reruns
- path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.global.dist.txt
- md5sum: 69e29702ef01fd8f6c7a5468fc35a16a
- path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.region.dist.txt
- md5sum: 6ec49cd7d510c2eb3d9d90fdb79b783a
- path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.summary.txt
- md5sum: 103098d0bf76ed82d2b87d5f242b099a
- path: results/reports/mosdepth/sample3/sample3.recal.regions.bed.gz
- md5sum: b5888cf7395c57d39879a5faa6159eb3
- path: results/reports/mosdepth/sample3/sample3.recal.regions.bed.gz.csi
- md5sum: 9cb0ad7039a3b703d16ca7d5b835c0ee
- path: results/reports/samtools/sample3/sample3.recal.cram.stats
# conda changes md5sums for test
- path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.global.dist.txt
- md5sum: f2dcd00a64947c49e8e4b93c2f4fbf27
- path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.region.dist.txt
- md5sum: 39005ffaac22871ffaaf19656fe69c5b
- path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.summary.txt
- md5sum: 68d4b98f17361fddf73052ead34fa370
- path: results/reports/mosdepth/sample4/sample4.recal.regions.bed.gz
- md5sum: 2819e995eafded35f53328c4ec19ba58
- path: results/reports/mosdepth/sample4/sample4.recal.regions.bed.gz.csi
- md5sum: 393c2749068304d8545b501b9d4658e4
- path: results/reports/samtools/sample4/sample4.recal.cram.stats
# conda changes md5sums for test
- name: Run joint calling on tumor only samples with mutect2
- command: nextflow run main.nf -profile test_cache,tools_tumoronly --input tests/csv/3.0/recalibrated_tumoronly_joint.csv --tools mutect2 --joint_mutect2 --outdir results
+ command: nextflow run main.nf -profile test,tools_tumoronly --input tests/csv/3.0/recalibrated_tumoronly_joint.csv --tools mutect2 --joint_mutect2 --outdir results
tags:
- mutect2_manual
- manual
@@ -239,19 +211,14 @@
- path: results/variant_calling/mutect2/test/test.mutect2.vcf.gz.tbi
# binary changes md5sums on reruns
- path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.global.dist.txt
- md5sum: f2dcd00a64947c49e8e4b93c2f4fbf27
- path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.region.dist.txt
- md5sum: 39005ffaac22871ffaaf19656fe69c5b
- path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.summary.txt
- md5sum: 68d4b98f17361fddf73052ead34fa370
- path: results/reports/mosdepth/sample3/sample3.recal.regions.bed.gz
- md5sum: 2819e995eafded35f53328c4ec19ba58
- path: results/reports/mosdepth/sample3/sample3.recal.regions.bed.gz.csi
- md5sum: 393c2749068304d8545b501b9d4658e4
- path: results/reports/samtools/sample3/sample3.recal.cram.stats
# conda changes md5sums for test
- name: Run joint calling on somatic samples with mutect2
- command: nextflow run main.nf -profile test_cache,tools_somatic --input tests/csv/3.0/recalibrated_somatic_joint.csv --tools mutect2 --joint_mutect2 --outdir results
+ command: nextflow run main.nf -profile test,tools_somatic --input tests/csv/3.0/recalibrated_somatic_joint.csv --tools mutect2 --joint_mutect2 --outdir results
tags:
- mutect2_manual
- somatic
@@ -299,39 +266,24 @@
- path: results/variant_calling/mutect2/test/test.mutect2.vcf.gz.tbi
# binary changes md5sums on reruns
- path: results/reports/mosdepth/sample1/sample1.recal.mosdepth.global.dist.txt
- md5sum: 69e29702ef01fd8f6c7a5468fc35a16a
- path: results/reports/mosdepth/sample1/sample1.recal.mosdepth.region.dist.txt
- md5sum: 6ec49cd7d510c2eb3d9d90fdb79b783a
- path: results/reports/mosdepth/sample1/sample1.recal.mosdepth.summary.txt
- md5sum: 103098d0bf76ed82d2b87d5f242b099a
- path: results/reports/mosdepth/sample1/sample1.recal.regions.bed.gz
- md5sum: b5888cf7395c57d39879a5faa6159eb3
- path: results/reports/mosdepth/sample1/sample1.recal.regions.bed.gz.csi
- md5sum: 9cb0ad7039a3b703d16ca7d5b835c0ee
- path: results/reports/samtools/sample1/sample1.recal.cram.stats
# conda changes md5sums for test
- path: results/reports/mosdepth/sample2/sample2.recal.mosdepth.global.dist.txt
- md5sum: f2dcd00a64947c49e8e4b93c2f4fbf27
- path: results/reports/mosdepth/sample2/sample2.recal.mosdepth.region.dist.txt
- md5sum: 39005ffaac22871ffaaf19656fe69c5b
- path: results/reports/mosdepth/sample2/sample2.recal.mosdepth.summary.txt
- md5sum: 68d4b98f17361fddf73052ead34fa370
- path: results/reports/mosdepth/sample2/sample2.recal.regions.bed.gz
- md5sum: 2819e995eafded35f53328c4ec19ba58
- path: results/reports/mosdepth/sample2/sample2.recal.regions.bed.gz.csi
- md5sum: 393c2749068304d8545b501b9d4658e4
- path: results/reports/samtools/sample2/sample2.recal.cram.stats
# conda changes md5sums for test
- path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.global.dist.txt
- md5sum: f2dcd00a64947c49e8e4b93c2f4fbf27
- path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.region.dist.txt
- md5sum: 39005ffaac22871ffaaf19656fe69c5b
- path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.summary.txt
- md5sum: 68d4b98f17361fddf73052ead34fa370
- path: results/reports/mosdepth/sample3/sample3.recal.regions.bed.gz
- md5sum: 2819e995eafded35f53328c4ec19ba58
- path: results/reports/mosdepth/sample3/sample3.recal.regions.bed.gz.csi
- md5sum: 393c2749068304d8545b501b9d4658e4
- path: results/reports/samtools/sample3/sample3.recal.cram.stats
# conda changes md5sums for test
- name: Run full pipeline on tumoronly with most tools
diff --git a/tests/test_tumor_normal_pair.yml b/tests/test_tumor_normal_pair.yml
index b616fc2b83..711e494ca1 100644
--- a/tests/test_tumor_normal_pair.yml
+++ b/tests/test_tumor_normal_pair.yml
@@ -1,5 +1,5 @@
- name: Run default pipeline for tumor normal pair
- command: nextflow run main.nf -profile test_cache,pair --outdir results
+ command: nextflow run main.nf -profile test,pair --outdir results
tags:
- default_extended
- preprocessing
@@ -39,45 +39,25 @@
- path: results/reports/markduplicates/test2/test2.md.cram.metrics
contains: ["test2 10103 880 35 523579 4837 2 0 0.408076 193306", "1.0 1 876 876", "100.0 80.515303 0 0"]
- path: results/reports/mosdepth/test/test.md.mosdepth.global.dist.txt
- md5sum: 76fa71922a3f748e507c2364c531dfcb
- path: results/reports/mosdepth/test/test.md.mosdepth.region.dist.txt
- md5sum: abc5df85e302b79985627888870882da
- path: results/reports/mosdepth/test/test.md.mosdepth.summary.txt
- md5sum: d536456436eb275159b8c6af83213d80
- path: results/reports/mosdepth/test/test.md.regions.bed.gz
- md5sum: 38fe39894abe62e38f8ac214cba64f2b
- path: results/reports/mosdepth/test/test.md.regions.bed.gz.csi
- md5sum: b1c2a861f64e20a94108a6de3b76c582
- path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt
- md5sum: 76fa71922a3f748e507c2364c531dfcb
- path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt
- md5sum: abc5df85e302b79985627888870882da
- path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt
- md5sum: d536456436eb275159b8c6af83213d80
- path: results/reports/mosdepth/test/test.recal.regions.bed.gz
- md5sum: 38fe39894abe62e38f8ac214cba64f2b
- path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi
- md5sum: b1c2a861f64e20a94108a6de3b76c582
- path: results/reports/mosdepth/test2/test2.md.mosdepth.global.dist.txt
- md5sum: 2020cf6dfc7ddca020c921dd9f0549b7
- path: results/reports/mosdepth/test2/test2.md.mosdepth.region.dist.txt
- md5sum: 38ff8b38c33b9231f047fea8ea830aae
- path: results/reports/mosdepth/test2/test2.md.mosdepth.summary.txt
- md5sum: 8b991358768cade225470a07cd34f573
- path: results/reports/mosdepth/test2/test2.md.regions.bed.gz
- md5sum: 5d67bc6ea9f077abb4fdac3b087c6387
- path: results/reports/mosdepth/test2/test2.md.regions.bed.gz.csi
- md5sum: d5f1c9389ecf52ba839e834780a94549
- path: results/reports/mosdepth/test2/test2.recal.mosdepth.global.dist.txt
- md5sum: 2020cf6dfc7ddca020c921dd9f0549b7
- path: results/reports/mosdepth/test2/test2.recal.mosdepth.region.dist.txt
- md5sum: 38ff8b38c33b9231f047fea8ea830aae
- path: results/reports/mosdepth/test2/test2.recal.mosdepth.summary.txt
- md5sum: 8b991358768cade225470a07cd34f573
- path: results/reports/mosdepth/test2/test2.recal.regions.bed.gz
- md5sum: 5d67bc6ea9f077abb4fdac3b087c6387
- path: results/reports/mosdepth/test2/test2.recal.regions.bed.gz.csi
- md5sum: d5f1c9389ecf52ba839e834780a94549
- path: results/reports/samtools/test/test.md.cram.stats
# conda changes md5sums for test
- path: results/reports/samtools/test/test.recal.cram.stats
diff --git a/tests/test_umi.yml b/tests/test_umi.yml
index 0034d131d9..0c8392f40e 100644
--- a/tests/test_umi.yml
+++ b/tests/test_umi.yml
@@ -1,5 +1,5 @@
- name: Run UMI test
- command: nextflow run main.nf -profile test_cache,umi --outdir results
+ command: nextflow run main.nf -profile test,umi --outdir results
tags:
- preprocessing
- umi
@@ -27,32 +27,22 @@
- path: results/reports/markduplicates/test/test.md.cram.metrics
contains: ["test 0 2804 3 4 0 77 0 0.027461 50115", "1.0 1 2651 2651", "12.0 8.9868 0 0"]
- path: results/reports/mosdepth/test/test.md.mosdepth.global.dist.txt
- md5sum: 09d22913aa50a0207f97a3f85b182c6e
- path: results/reports/mosdepth/test/test.md.mosdepth.region.dist.txt
- md5sum: 9359ba1c4e09aa47cc95c9134f526675
- path: results/reports/mosdepth/test/test.md.mosdepth.summary.txt
- md5sum: 9bbea5e4d213a51f501c2aadff8d4526
- path: results/reports/mosdepth/test/test.md.regions.bed.gz
- md5sum: ef4426cd1d433464004bb39d483abad9
- path: results/reports/mosdepth/test/test.md.regions.bed.gz.csi
- md5sum: d0713716f63ac573f4a3385733e9a537
- path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt
- md5sum: 09d22913aa50a0207f97a3f85b182c6e
- path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt
- md5sum: 9359ba1c4e09aa47cc95c9134f526675
- path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt
- md5sum: 9bbea5e4d213a51f501c2aadff8d4526
- path: results/reports/mosdepth/test/test.recal.regions.bed.gz
- md5sum: ef4426cd1d433464004bb39d483abad9
- path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi
- md5sum: d0713716f63ac573f4a3385733e9a537
- path: results/reports/samtools/test/test.md.cram.stats
# text-based file changes md5sums on reruns
- path: results/reports/samtools/test/test.recal.cram.stats
# text-based file changes md5sums on reruns
- name: Run Sentieon-FGBio UMI combination test
- command: nextflow run main.nf -profile test_cache,software_license,umi --sentieon_extension --outdir results --aligner "sentieon-bwamem"
+ command: nextflow run main.nf -profile test,software_license,umi --sentieon_extension --outdir results --aligner "sentieon-bwamem"
tags:
- preprocessing
- umi
@@ -61,7 +51,7 @@
contains:
- "Sentieon BWA is currently not compatible with FGBio UMI handeling. Please choose a different aligner."
# - name: Run UMI TSO test
-# command: nextflow run main.nf -profile test_cache,umi_tso --outdir results
+# command: nextflow run main.nf -profile test,umi_tso --outdir results
# tags:
# - umi_tso
# - umi
diff --git a/workflows/sarek/main.nf b/workflows/sarek/main.nf
index 5062470373..164a44f45e 100644
--- a/workflows/sarek/main.nf
+++ b/workflows/sarek/main.nf
@@ -106,7 +106,7 @@ workflow SAREK {
gc_file
germline_resource
germline_resource_tbi
- index_alignement
+ index_alignment
intervals_and_num_intervals
intervals_bed_combined
intervals_bed_combined_for_variant_calling
@@ -188,7 +188,7 @@ workflow SAREK {
input_fastq,
fasta,
fasta_fai,
- index_alignement,
+ index_alignment,
params.group_by_umi_strategy)
bam_converted_from_fastq = FASTQ_CREATE_UMI_CONSENSUS_FGBIO.out.consensusbam.map{ meta, bam -> [ meta, bam, [] ] }
@@ -255,7 +255,7 @@ workflow SAREK {
// reads will be sorted
sort_bam = true
- FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON(reads_for_alignment, index_alignement, sort_bam, fasta, fasta_fai)
+ FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON(reads_for_alignment, index_alignment, sort_bam, fasta, fasta_fai)
// Grouping the bams from the same samples not to stall the workflow
// Use groupKey to make sure that the correct group can advance as soon as it is complete
@@ -879,7 +879,7 @@ workflow SAREK {
ch_multiqc_files = ch_multiqc_files.mix(ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml'))
ch_multiqc_files = ch_multiqc_files.mix(version_yaml)
ch_multiqc_files = ch_multiqc_files.mix(reports)
- ch_multiqc_files = ch_multiqc_files.mix(ch_methods_description.collectFile(name: 'methods_description_mqc.yaml', sort: false))
+ ch_multiqc_files = ch_multiqc_files.mix(ch_methods_description.collectFile(name: 'methods_description_mqc.yaml', sort: true))
MULTIQC (
ch_multiqc_files.collect(),