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master branch #4

Merged
merged 19 commits into from
Mar 11, 2024
Merged

master branch #4

merged 19 commits into from
Mar 11, 2024

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y-popov
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@y-popov y-popov commented Mar 11, 2024

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y-popov and others added 19 commits November 3, 2023 10:22
@y-popov
HGI config
16682bb
@y-popov
tools optimisation
56d54d0
@y-popov
haplotypecaller_vc tools added
df2c140
@y-popov
haplotypecaller_jc tools added
a63f0c6
@Sanger-ad7
Changed config order
da274a5
@Sanger-ad7
Added improved schema
f68a108
@Sanger-ad7
changed interval split to notspan chromosomes
9089209
@Sanger-ad7
Added LSF specifics to impoertGVF and genotypeGVCF
961c272
@Sanger-ad7
Added -XX:+UseSerialGC to gatk modules and lsf config update
0f41fb6
@Sanger-ad7
typo in genomicsdbimport
69668ea
@Sanger-ad7
typo in genotypegvcfs
8c230fd
@Sanger-ad7
Corrected bed split script
4690038
@Sanger-ad7
Made everything retry
3ee04f0
@Sanger-ad7
updated schema
2c05a90
@Sanger-ad7
Removed tmp_dir from import and genotype plus added lsf tmp resource
790afe4
@Sanger-ad7
Corrected genomicDBimport
38a103d
@y-popov
fine tuning
85f83f0
@y-popov
Merge branch 'ad7-caller-split' into ip13-caller-split
b46969f 
# Conflicts:
#	conf/hgi.config
@y-popov
reverted some changes back
8899350 
- made hgi to be a profile again to make our changes less destructive
- moved error strategy from 'base' to 'hgi' config for the same reason
- changed error fall-back strategy from 'ignore' to 'finish' in order to make all errors crystal clear visible
@y-popov y-popov merged commit 8899350 into hgi_master Mar 11, 2024
52 of 66 checks passed
@y-popov y-popov deleted the ip13 branch March 11, 2024 14:37
@github-actions GitHub Actions
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nf-core lint overall result: Failed ❌

Posted for pipeline commit 8899350

+| ✅ 162 tests passed       |+
#| ❔   7 tests were ignored |#
!| ❗   8 tests had warnings |!
-| ❌  42 tests failed       |-

❌ Test failures:

  • files_exist - File must be removed: lib/Utils.groovy
  • files_exist - File must be removed: lib/WorkflowMain.groovy
  • files_exist - File must be removed: lib/NfcoreTemplate.groovy
  • files_exist - File must be removed: lib/WorkflowSarek.groovy
  • files_exist - File must be removed: lib/nfcore_external_java_deps.jar
  • nextflow_config - Config default value incorrect: params.step is set as variant_calling in nextflow_schema.json but is mapping in nextflow.config.
  • nextflow_config - Config default value incorrect: params.nucleotides_per_second is set as 40000.0 in nextflow_schema.json but is 200000 in nextflow.config.
  • nextflow_config - Config default value incorrect: params.igenomes_base is set as s3://ngi-igenomes/igenomes/ in nextflow_schema.json but is s3://ngi-igenomes/igenomes in nextflow.config.
  • nextflow_config - Default value from the Nextflow schema params.tracedir = 25.MB`` not found in nextflow.config.
  • files_unchanged - .github/CONTRIBUTING.md does not match the template
  • files_unchanged - .github/PULL_REQUEST_TEMPLATE.md does not match the template
  • files_unchanged - .github/workflows/branch.yml does not match the template
  • files_unchanged - .github/workflows/linting_comment.yml does not match the template
  • files_unchanged - .github/workflows/linting.yml does not match the template
  • files_unchanged - assets/email_template.html does not match the template
  • files_unchanged - assets/email_template.txt does not match the template
  • files_unchanged - pyproject.toml does not match the template
  • schema_params - Param build_only_index from nextflow config not found in nextflow_schema.json
  • schema_params - Param download_cache from nextflow config not found in nextflow_schema.json
  • schema_params - Param save_mapped from nextflow config not found in nextflow_schema.json
  • schema_params - Param cnvkit_reference from nextflow config not found in nextflow_schema.json
  • schema_params - Param concatenate_vcfs from nextflow config not found in nextflow_schema.json
  • schema_params - Param joint_mutect2 from nextflow config not found in nextflow_schema.json
  • schema_params - Param sentieon_haplotyper_emit_mode from nextflow config not found in nextflow_schema.json
  • schema_params - Param outdir_cache from nextflow config not found in nextflow_schema.json
  • schema_params - Param use_annotation_cache_keys from nextflow config not found in nextflow_schema.json
  • schema_params - Param vep_custom_args from nextflow config not found in nextflow_schema.json
  • schema_params - Param multiqc_logo from nextflow config not found in nextflow_schema.json
  • schema_params - Param multiqc_methods_description from nextflow config not found in nextflow_schema.json
  • schema_params - Param hook_url from nextflow config not found in nextflow_schema.json
  • schema_params - Param version from nextflow config not found in nextflow_schema.json
  • schema_params - Param test_data_base from nextflow config not found in nextflow_schema.json
  • schema_params - Param validationFailUnrecognisedParams from nextflow config not found in nextflow_schema.json
  • schema_params - Param validationLenientMode from nextflow config not found in nextflow_schema.json
  • schema_params - Param validationShowHiddenParams from nextflow config not found in nextflow_schema.json
  • schema_params - Param input_restart from nextflow config not found in nextflow_schema.json
  • schema_params - Default value for param save_bam_mapped invalid: Not in pipeline parameters. Check nextflow.config.
  • schema_params - Default value for param snpeff_version invalid: Not in pipeline parameters. Check nextflow.config.
  • schema_params - Default value for param vep_version invalid: Not in pipeline parameters. Check nextflow.config.
  • schema_params - Default value for param tracedir invalid: Not in pipeline parameters. Check nextflow.config.
  • schema_params - Default value for param show_hidden_params invalid: Not in pipeline parameters. Check nextflow.config.
  • schema_params - Default value for param enable_conda invalid: Not in pipeline parameters. Check nextflow.config.

❗ Test warnings:

  • nextflow_config - Config manifest.version should end in dev: 3.3.2
  • pipeline_todos - TODO string in WorkflowSarek.groovy: Optionally add in-text citation tools to this list.
  • schema_params - Schema param save_bam_mapped not found from nextflow config
  • schema_params - Schema param snpeff_version not found from nextflow config
  • schema_params - Schema param vep_version not found from nextflow config
  • schema_params - Schema param tracedir not found from nextflow config
  • schema_params - Schema param show_hidden_params not found from nextflow config
  • schema_params - Schema param enable_conda not found from nextflow config

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.13.1
  • Run at 2024-03-11 14:53:36

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2 participants
@y-popov @Sanger-ad7