diff --git a/CHANGELOG.md b/CHANGELOG.md
index 45337c089f..4a583aaf26 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -41,6 +41,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
### Removed
- [1656](https://github.com/nf-core/sarek/pull/1656) - Retiring parameter `snpeff_genome`
+- [1709](https://github.com/nf-core/sarek/pull/1709) - Remove `Strelka` tumor-only somatic variant calling
### Dependencies
diff --git a/docs/images/sarek_subway.png b/docs/images/sarek_subway.png
index a419afa6ac..f70415fbfe 100644
Binary files a/docs/images/sarek_subway.png and b/docs/images/sarek_subway.png differ
diff --git a/docs/images/sarek_subway.svg b/docs/images/sarek_subway.svg
index af4544e18e..d5129c4b36 100644
--- a/docs/images/sarek_subway.svg
+++ b/docs/images/sarek_subway.svg
@@ -33,11 +33,11 @@
inkscape:document-units="mm"
showgrid="true"
inkscape:zoom="1"
- inkscape:cx="621.99998"
- inkscape:cy="435.49999"
+ inkscape:cx="621.5"
+ inkscape:cy="435.5"
inkscape:window-width="1854"
inkscape:window-height="1011"
- inkscape:window-x="1986"
+ inkscape:window-x="66"
inkscape:window-y="32"
inkscape:window-maximized="1"
inkscape:current-layer="layer4"
@@ -2276,20 +2276,6 @@
x="568.87335"
sodipodi:role="line">mantastrelka2
-Output files for all single samples (normal or tumor-only)
+Output files for single samples (normal)
**Output directory: `{outdir}/variantcalling/strelka//`**
diff --git a/docs/usage.md b/docs/usage.md
index 6877ed196c..2d442c7e20 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -559,7 +559,7 @@ Some of the currently, available test profiles:
| no_intervals | `nextflow run main.nf -profile test_cache,no_intervals,docker` |
| targeted | `nextflow run main.nf -profile test_cache,targeted,docker` |
| tools_germline | `nextflow run main.nf -profile test_cache,tools_germline,docker --tools strelka` |
-| tools_tumoronly | `nextflow run main.nf -profile test_cache,tools_tumoronly,docker --tools strelka` |
+| tools_tumoronly | `nextflow run main.nf -profile test_cache,tools_tumoronly,docker --tools mutect2` |
| tools_somatic | `nextflow run main.nf -profile test_cache,tools_somatic,docker --tools strelka` |
| trimming | `nextflow run main.nf -profile test_cache,trim_fastq,docker` |
| umi | `nextflow run main.nf -profile test_cache,umi,docker` |
@@ -583,7 +583,7 @@ This list is by no means exhaustive and it will depend on the specific analysis
| [GATK Mutect2](https://gatk.broadinstitute.org/hc/en-us/articles/5358911630107-Mutect2) | x | x | x | - | x | x |
| [lofreq](https://github.com/CSB5/lofreq) | x | x | x | - | x | - |
| [mpileup](https://www.htslib.org/doc/samtools-mpileup.html) | x | x | x | x | x | - |
-| [Strelka](https://github.com/Illumina/strelka) | x | x | x | x | x | x |
+| [Strelka](https://github.com/Illumina/strelka) | x | x | x | x | - | x |
| [Manta](https://github.com/Illumina/manta) | x | x | x | x | x | x |
| [TIDDIT](https://github.com/SciLifeLab/TIDDIT) | x | x | x | x | x | x |
| [ASCAT](https://github.com/VanLoo-lab/ascat) | x | x | - | - | - | x |
diff --git a/subworkflows/local/bam_variant_calling_tumor_only_all/main.nf b/subworkflows/local/bam_variant_calling_tumor_only_all/main.nf
index c9f1093047..8016391cfc 100644
--- a/subworkflows/local/bam_variant_calling_tumor_only_all/main.nf
+++ b/subworkflows/local/bam_variant_calling_tumor_only_all/main.nf
@@ -6,7 +6,6 @@
include { BAM_VARIANT_CALLING_CNVKIT } from '../bam_variant_calling_cnvkit/main'
include { BAM_VARIANT_CALLING_FREEBAYES } from '../bam_variant_calling_freebayes/main'
include { BAM_VARIANT_CALLING_MPILEUP } from '../bam_variant_calling_mpileup/main'
-include { BAM_VARIANT_CALLING_SINGLE_STRELKA } from '../bam_variant_calling_single_strelka/main'
include { BAM_VARIANT_CALLING_SINGLE_TIDDIT } from '../bam_variant_calling_single_tiddit/main'
include { BAM_VARIANT_CALLING_TUMOR_ONLY_CONTROLFREEC } from '../bam_variant_calling_tumor_only_controlfreec/main'
include { BAM_VARIANT_CALLING_TUMOR_ONLY_MANTA } from '../bam_variant_calling_tumor_only_manta/main'
@@ -46,7 +45,6 @@ workflow BAM_VARIANT_CALLING_TUMOR_ONLY_ALL {
vcf_manta = Channel.empty()
vcf_mpileup = Channel.empty()
vcf_mutect2 = Channel.empty()
- vcf_strelka = Channel.empty()
vcf_tiddit = Channel.empty()
vcf_lofreq = Channel.empty()
@@ -164,20 +162,6 @@ workflow BAM_VARIANT_CALLING_TUMOR_ONLY_ALL {
versions = versions.mix(BAM_VARIANT_CALLING_TUMOR_ONLY_MANTA.out.versions)
}
- // STRELKA
- if (tools.split(',').contains('strelka')) {
- BAM_VARIANT_CALLING_SINGLE_STRELKA(
- cram,
- dict,
- fasta.map{ meta, fasta -> [ fasta ] },
- fasta_fai.map{ meta, fasta_fai -> [ fasta_fai ] },
- intervals_bed_gz_tbi
- )
-
- vcf_strelka = BAM_VARIANT_CALLING_SINGLE_STRELKA.out.vcf
- versions = versions.mix(BAM_VARIANT_CALLING_SINGLE_STRELKA.out.versions)
- }
-
// TIDDIT
if (tools.split(',').contains('tiddit')) {
BAM_VARIANT_CALLING_SINGLE_TIDDIT(
@@ -195,7 +179,6 @@ workflow BAM_VARIANT_CALLING_TUMOR_ONLY_ALL {
vcf_manta,
vcf_mutect2,
vcf_mpileup,
- vcf_strelka,
vcf_tiddit
)
@@ -206,7 +189,6 @@ workflow BAM_VARIANT_CALLING_TUMOR_ONLY_ALL {
vcf_manta
vcf_mpileup
vcf_mutect2
- vcf_strelka
vcf_tiddit
versions = versions
diff --git a/tests/config/pytesttags.yml b/tests/config/pytesttags.yml
index a691b4019b..bf67e8358c 100644
--- a/tests/config/pytesttags.yml
+++ b/tests/config/pytesttags.yml
@@ -389,7 +389,6 @@ strelka:
- subworkflows/local/bam_variant_calling_single_strelka/**
- subworkflows/local/bam_variant_calling_somatic_all/**
- subworkflows/local/bam_variant_calling_somatic_strelka/**
- - subworkflows/local/bam_variant_calling_tumor_only_all/**
- tests/csv/3.0/recalibrated_germline.csv
- tests/csv/3.0/recalibrated_somatic.csv
- tests/csv/3.0/recalibrated_tumoronly.csv
@@ -408,7 +407,6 @@ strelka_bp:
- subworkflows/local/bam_variant_calling_somatic_all/**
- subworkflows/local/bam_variant_calling_somatic_manta/**
- subworkflows/local/bam_variant_calling_somatic_strelka/**
- - subworkflows/local/bam_variant_calling_tumor_only_all/**
- tests/csv/3.0/recalibrated_somatic.csv
- tests/test_strelka_bp.yml
@@ -463,7 +461,6 @@ concatenate_vcfs:
- subworkflows/local/bam_variant_calling_germline_manta/**
- subworkflows/local/bam_variant_calling_haplotypecaller/**
- subworkflows/local/bam_variant_calling_mpileup/**
- - subworkflows/local/bam_variant_calling_single_strelka/**
- subworkflows/local/bam_variant_calling_single_tiddit/**
- subworkflows/local/bam_variant_calling_somatic_all/**
- subworkflows/local/bam_variant_calling_tumor_only_all/**
diff --git a/tests/test_strelka.yml b/tests/test_strelka.yml
index b2b25672a2..57ddd2d67b 100644
--- a/tests/test_strelka.yml
+++ b/tests/test_strelka.yml
@@ -176,80 +176,6 @@
- path: results/reports/mosdepth/sample1/sample1.recal.per-base.bed.gz
- path: results/reports/mosdepth/sample1/sample1.recal.per-base.bed.gz.csi
- 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,tools_tumoronly --tools strelka --outdir results
- tags:
- - strelka
- - tumor_only
- - variant_calling
- files:
- - path: results/csv/variantcalled.csv
- md5sum: 8d2a5e0ad12781c99e773b828e478d35
- - path: results/multiqc
- - path: results/reports/bcftools/strelka/sample2/sample2.strelka.variants.bcftools_stats.txt
- # conda changes md5sums for test
- - path: results/reports/vcftools/strelka/sample2/sample2.strelka.variants.FILTER.summary
- md5sum: fa3112841a4575d104916027c8851b30
- - path: results/reports/vcftools/strelka/sample2/sample2.strelka.variants.TsTv.count
- md5sum: d7f54d09d38af01a574a4930af21cfc9
- - path: results/reports/vcftools/strelka/sample2/sample2.strelka.variants.TsTv.qual
- contains: ["19 453 47848 0.00946748 11 50 0.22", "72 458 47880 0.00956558 6 20 0.3", "314 463 47899 0.00966617 1 1 1"]
- - path: results/variant_calling/strelka/sample2/sample2.strelka.genome.vcf.gz
- # binary changes md5sums on reruns
- - path: results/variant_calling/strelka/sample2/sample2.strelka.genome.vcf.gz.tbi
- # binary changes md5sums on reruns
- - path: results/variant_calling/strelka/sample2/sample2.strelka.variants.vcf.gz
- # binary changes md5sums on reruns
- - path: results/variant_calling/strelka/sample2/sample2.strelka.variants.vcf.gz.tbi
- # binary changes md5sums on reruns
- - path: results/strelka
- should_exist: false
- - path: results/reports/mosdepth/sample2/sample2.recal.mosdepth.global.dist.txt
- - path: results/reports/mosdepth/sample2/sample2.recal.mosdepth.region.dist.txt
- - path: results/reports/mosdepth/sample2/sample2.recal.mosdepth.summary.txt
- - path: results/reports/mosdepth/sample2/sample2.recal.regions.bed.gz
- - path: results/reports/mosdepth/sample2/sample2.recal.regions.bed.gz.csi
- - 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,tools_tumoronly --tools strelka --no_intervals --outdir results
- tags:
- - no_intervals
- - strelka
- - tumor_only
- - variant_calling
- files:
- - path: results/csv/variantcalled.csv
- md5sum: 8d2a5e0ad12781c99e773b828e478d35
- - path: results/multiqc
- - path: results/no_intervals.bed
- md5sum: f3dac01ea66b95fe477446fde2d31489
- - path: results/no_intervals.bed.gz
- md5sum: f3dac01ea66b95fe477446fde2d31489
- - path: results/no_intervals.bed.gz.tbi
- md5sum: f3dac01ea66b95fe477446fde2d31489
- - path: results/reports/bcftools/strelka/sample2/sample2.strelka.variants.bcftools_stats.txt
- # conda changes md5sums for test
- - path: results/reports/vcftools/strelka/sample2/sample2.strelka.variants.FILTER.summary
- md5sum: d1dcce19d82ced016724ace746e95d01
- - path: results/reports/vcftools/strelka/sample2/sample2.strelka.variants.TsTv.count
- md5sum: 9de35bbe9ebe45166b6bd195717f733a
- - path: results/reports/vcftools/strelka/sample2/sample2.strelka.variants.TsTv.qual
- # conda changes md5sums for test
- - path: results/variant_calling/strelka/sample2/sample2.strelka.genome.vcf.gz
- # binary changes md5sums on reruns
- - path: results/variant_calling/strelka/sample2/sample2.strelka.genome.vcf.gz.tbi
- # binary changes md5sums on reruns
- - path: results/variant_calling/strelka/sample2/sample2.strelka.variants.vcf.gz
- # binary changes md5sums on reruns
- - path: results/variant_calling/strelka/sample2/sample2.strelka.variants.vcf.gz.tbi
- # binary changes md5sums on reruns
- - path: results/strelka
- should_exist: false
- - path: results/reports/mosdepth/sample2/sample2.recal.mosdepth.global.dist.txt
- - path: results/reports/mosdepth/sample2/sample2.recal.mosdepth.summary.txt
- - path: results/reports/mosdepth/sample2/sample2.recal.per-base.bed.gz
- - path: results/reports/mosdepth/sample2/sample2.recal.per-base.bed.gz.csi
- - 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,tools_somatic --tools strelka --outdir results
tags:
diff --git a/tests/test_tools_manually.yml b/tests/test_tools_manually.yml
index fe1642b3c3..19e519e268 100644
--- a/tests/test_tools_manually.yml
+++ b/tests/test_tools_manually.yml
@@ -287,7 +287,7 @@
- path: results/reports/samtools/sample3/sample3.recal.cram.stats
# conda changes md5sums for test
- name: Run full pipeline on tumoronly with most tools
- command: nextflow run . -profile test --input tests/csv/3.0/fastq_tumor_only.csv --tools cnvkit,freebayes,merge,mpileup,mutect2,snpeff,strelka,tiddit,vep --outdir results
+ command: nextflow run . -profile test --input tests/csv/3.0/fastq_tumor_only.csv --tools cnvkit,freebayes,merge,mpileup,mutect2,snpeff,tiddit,vep --outdir results
tags:
- full_pipeline_manual
- manual