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uclahs-cds / pipeline-call-sSNV

A Nextflow pipeline to identify the somatic single nucleotide variants (sSNVs) by comparing a pair of tumor/normal samples.
https://uclahs-cds.github.io/pipeline-call-sSNV/
GNU General Public License v2.0
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Bump external/pipeline-Nextflow-module from `9db08f0` to `4597ebc` #290

Closed dependabot[bot] closed 6 months ago

dependabot[bot] commented 6 months ago

Bumps external/pipeline-Nextflow-module from 9db08f0 to 4597ebc.

Commits
  • 4597ebc Merge pull request #40 from uclahs-cds/nwiltsie-static-upgrade
  • 63a022a Upgrade to latest static analysis Action
  • See full diff in compare view


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github-actions[bot] commented 6 months ago

Bleep bloop, I am a robot.

Alas, some of the Nextflow configuration tests failed!

test/configtest-F16.json

@ ["params_schema"]
+ {"algorithm":{"choices":["mutect2","somaticsniper","strelka2","muse"],"default":["mutect2","somaticsniper","strelka2","muse"],"help":"List of sSNV algorithms","required":true,"type":"List"},"base_resource_update":{"elements":{"cpus":{"help":"List of CPU updates","required":false,"type":"ResourceUpdateList"},"memory":{"help":"List of memory updates","required":false,"type":"ResourceUpdateList"}},"help":"User-defined modifications for adjusting base resource allocations for processes","required":false,"type":"ResourceUpdateNamespace"},"bgzip_extra_args":{"allow_empty":true,"default":"","help":"Additional arguments for bgzip command","required":false,"type":"String"},"dataset_id":{"help":"Dataset identifier","required":true,"type":"String"},"dbSNP":{"help":"","mode":"r","required":true,"type":"Path"},"exome":{"default":false,"help":"The exome option when running manta and strelka2","required":false,"type":"Bool"},"filter_mutect_calls_extra_args":{"allow_empty":true,"help":"Additional arguments for the FilterMutectCalls command","required":false,"type":"String"},"germline_resource_gnomad_vcf":{"allow_empty":true,"help":"","mode":"r","required":false,"type":"Path"},"input":{"elements":{"normal":{"elements":{"BAM":{"help":"Absolute path to normal sample BAM files","mode":"r","required":true,"type":"Path"}},"help":"Normal id/path input","required":false,"type":"BAMEntryList"},"tumor":{"elements":{"BAM":{"help":"Absolute path to tumor sample BAM files","mode":"r","required":true,"type":"Path"},"contamination_table":{"help":"Absolute path to contamination.tables","mode":"r","required":false,"type":"Path"}},"help":"Tumor id/path input","required":true,"type":"BAMEntryList"}},"help":"Input samples","required":true,"type":"InputNamespace"},"intersect_regions":{"help":"call regions bed file used by mutect2, strelka2 and intersect","mode":"r","required":true,"type":"Path"},"mutect2_extra_args":{"allow_empty":true,"help":"Additional arguments for the Mutect2 command","required":false,"type":"String"},"ncbi_build":{"help":"NCBI build version, e.g. GRCh38","required":true,"type":"String"},"output_dir":{"help":"Absolute path to output directory","mode":"w","required":true,"type":"Path"},"patient_id":{"help":"Patient identifier","required":true,"type":"String"},"reference":{"help":"Absolute path to reference directory","mode":"r","required":true,"type":"Path"},"save_intermediate_files":{"default":false,"help":"The option to save the intermediate files","required":false,"type":"Bool"},"scatter_count":{"help":"","required":true,"type":"Integer"},"split_intervals_extra_args":{"allow_empty":true,"help":"Additional arguments for the SplitIntervals command","required":false,"type":"String"},"tabix_extra_args":{"allow_empty":true,"default":"","help":"Additional arguments for tabix command","required":false,"type":"String"},"vcf2maf_extra_args":{"allow_empty":true,"help":"Additional arguments for the vcf2maf command","required":false,"type":"String"},"work_dir":{"help":"Absolute path to output directory","mode":"w","required":false,"type":"Path"}}
@ ["proc_names"]
+ "[Ljava.lang.String;@dec0ded"
@ ["yaml"]
+ {"algorithm":{"choices":["mutect2","somaticsniper","strelka2","muse"],"default":["mutect2","somaticsniper","strelka2","muse"],"help":"List of sSNV algorithms","required":true,"type":"List"},"base_resource_update":{"elements":{"cpus":{"help":"List of CPU updates","required":false,"type":"ResourceUpdateList"},"memory":{"help":"List of memory updates","required":false,"type":"ResourceUpdateList"}},"help":"User-defined modifications for adjusting base resource allocations for processes","required":false,"type":"ResourceUpdateNamespace"},"bgzip_extra_args":{"allow_empty":true,"default":"","help":"Additional arguments for bgzip command","required":false,"type":"String"},"dataset_id":{"help":"Dataset identifier","required":true,"type":"String"},"dbSNP":{"help":"","mode":"r","required":true,"type":"Path"},"exome":{"default":false,"help":"The exome option when running manta and strelka2","required":false,"type":"Bool"},"filter_mutect_calls_extra_args":{"allow_empty":true,"help":"Additional arguments for the FilterMutectCalls command","required":false,"type":"String"},"germline_resource_gnomad_vcf":{"allow_empty":true,"help":"","mode":"r","required":false,"type":"Path"},"input":{"elements":{"normal":{"elements":{"BAM":{"help":"Absolute path to normal sample BAM files","mode":"r","required":true,"type":"Path"}},"help":"Normal id/path input","required":false,"type":"BAMEntryList"},"tumor":{"elements":{"BAM":{"help":"Absolute path to tumor sample BAM files","mode":"r","required":true,"type":"Path"},"contamination_table":{"help":"Absolute path to contamination.tables","mode":"r","required":false,"type":"Path"}},"help":"Tumor id/path input","required":true,"type":"BAMEntryList"}},"help":"Input samples","required":true,"type":"InputNamespace"},"intersect_regions":{"help":"call regions bed file used by mutect2, strelka2 and intersect","mode":"r","required":true,"type":"Path"},"mutect2_extra_args":{"allow_empty":true,"help":"Additional arguments for the Mutect2 command","required":false,"type":"String"},"ncbi_build":{"help":"NCBI build version, e.g. GRCh38","required":true,"type":"String"},"output_dir":{"help":"Absolute path to output directory","mode":"w","required":true,"type":"Path"},"patient_id":{"help":"Patient identifier","required":true,"type":"String"},"reference":{"help":"Absolute path to reference directory","mode":"r","required":true,"type":"Path"},"save_intermediate_files":{"default":false,"help":"The option to save the intermediate files","required":false,"type":"Bool"},"scatter_count":{"help":"","required":true,"type":"Integer"},"split_intervals_extra_args":{"allow_empty":true,"help":"Additional arguments for the SplitIntervals command","required":false,"type":"String"},"tabix_extra_args":{"allow_empty":true,"default":"","help":"Additional arguments for tabix command","required":false,"type":"String"},"vcf2maf_extra_args":{"allow_empty":true,"help":"Additional arguments for the vcf2maf command","required":false,"type":"String"},"work_dir":{"help":"Absolute path to output directory","mode":"w","required":false,"type":"Path"}}

test/configtest-F32.json

@ ["params_schema"]
+ {"algorithm":{"choices":["mutect2","somaticsniper","strelka2","muse"],"default":["mutect2","somaticsniper","strelka2","muse"],"help":"List of sSNV algorithms","required":true,"type":"List"},"base_resource_update":{"elements":{"cpus":{"help":"List of CPU updates","required":false,"type":"ResourceUpdateList"},"memory":{"help":"List of memory updates","required":false,"type":"ResourceUpdateList"}},"help":"User-defined modifications for adjusting base resource allocations for processes","required":false,"type":"ResourceUpdateNamespace"},"bgzip_extra_args":{"allow_empty":true,"default":"","help":"Additional arguments for bgzip command","required":false,"type":"String"},"dataset_id":{"help":"Dataset identifier","required":true,"type":"String"},"dbSNP":{"help":"","mode":"r","required":true,"type":"Path"},"exome":{"default":false,"help":"The exome option when running manta and strelka2","required":false,"type":"Bool"},"filter_mutect_calls_extra_args":{"allow_empty":true,"help":"Additional arguments for the FilterMutectCalls command","required":false,"type":"String"},"germline_resource_gnomad_vcf":{"allow_empty":true,"help":"","mode":"r","required":false,"type":"Path"},"input":{"elements":{"normal":{"elements":{"BAM":{"help":"Absolute path to normal sample BAM files","mode":"r","required":true,"type":"Path"}},"help":"Normal id/path input","required":false,"type":"BAMEntryList"},"tumor":{"elements":{"BAM":{"help":"Absolute path to tumor sample BAM files","mode":"r","required":true,"type":"Path"},"contamination_table":{"help":"Absolute path to contamination.tables","mode":"r","required":false,"type":"Path"}},"help":"Tumor id/path input","required":true,"type":"BAMEntryList"}},"help":"Input samples","required":true,"type":"InputNamespace"},"intersect_regions":{"help":"call regions bed file used by mutect2, strelka2 and intersect","mode":"r","required":true,"type":"Path"},"mutect2_extra_args":{"allow_empty":true,"help":"Additional arguments for the Mutect2 command","required":false,"type":"String"},"ncbi_build":{"help":"NCBI build version, e.g. GRCh38","required":true,"type":"String"},"output_dir":{"help":"Absolute path to output directory","mode":"w","required":true,"type":"Path"},"patient_id":{"help":"Patient identifier","required":true,"type":"String"},"reference":{"help":"Absolute path to reference directory","mode":"r","required":true,"type":"Path"},"save_intermediate_files":{"default":false,"help":"The option to save the intermediate files","required":false,"type":"Bool"},"scatter_count":{"help":"","required":true,"type":"Integer"},"split_intervals_extra_args":{"allow_empty":true,"help":"Additional arguments for the SplitIntervals command","required":false,"type":"String"},"tabix_extra_args":{"allow_empty":true,"default":"","help":"Additional arguments for tabix command","required":false,"type":"String"},"vcf2maf_extra_args":{"allow_empty":true,"help":"Additional arguments for the vcf2maf command","required":false,"type":"String"},"work_dir":{"help":"Absolute path to output directory","mode":"w","required":false,"type":"Path"}}
@ ["proc_names"]
+ "[Ljava.lang.String;@dec0ded"
@ ["yaml"]
+ {"algorithm":{"choices":["mutect2","somaticsniper","strelka2","muse"],"default":["mutect2","somaticsniper","strelka2","muse"],"help":"List of sSNV algorithms","required":true,"type":"List"},"base_resource_update":{"elements":{"cpus":{"help":"List of CPU updates","required":false,"type":"ResourceUpdateList"},"memory":{"help":"List of memory updates","required":false,"type":"ResourceUpdateList"}},"help":"User-defined modifications for adjusting base resource allocations for processes","required":false,"type":"ResourceUpdateNamespace"},"bgzip_extra_args":{"allow_empty":true,"default":"","help":"Additional arguments for bgzip command","required":false,"type":"String"},"dataset_id":{"help":"Dataset identifier","required":true,"type":"String"},"dbSNP":{"help":"","mode":"r","required":true,"type":"Path"},"exome":{"default":false,"help":"The exome option when running manta and strelka2","required":false,"type":"Bool"},"filter_mutect_calls_extra_args":{"allow_empty":true,"help":"Additional arguments for the FilterMutectCalls command","required":false,"type":"String"},"germline_resource_gnomad_vcf":{"allow_empty":true,"help":"","mode":"r","required":false,"type":"Path"},"input":{"elements":{"normal":{"elements":{"BAM":{"help":"Absolute path to normal sample BAM files","mode":"r","required":true,"type":"Path"}},"help":"Normal id/path input","required":false,"type":"BAMEntryList"},"tumor":{"elements":{"BAM":{"help":"Absolute path to tumor sample BAM files","mode":"r","required":true,"type":"Path"},"contamination_table":{"help":"Absolute path to contamination.tables","mode":"r","required":false,"type":"Path"}},"help":"Tumor id/path input","required":true,"type":"BAMEntryList"}},"help":"Input samples","required":true,"type":"InputNamespace"},"intersect_regions":{"help":"call regions bed file used by mutect2, strelka2 and intersect","mode":"r","required":true,"type":"Path"},"mutect2_extra_args":{"allow_empty":true,"help":"Additional arguments for the Mutect2 command","required":false,"type":"String"},"ncbi_build":{"help":"NCBI build version, e.g. GRCh38","required":true,"type":"String"},"output_dir":{"help":"Absolute path to output directory","mode":"w","required":true,"type":"Path"},"patient_id":{"help":"Patient identifier","required":true,"type":"String"},"reference":{"help":"Absolute path to reference directory","mode":"r","required":true,"type":"Path"},"save_intermediate_files":{"default":false,"help":"The option to save the intermediate files","required":false,"type":"Bool"},"scatter_count":{"help":"","required":true,"type":"Integer"},"split_intervals_extra_args":{"allow_empty":true,"help":"Additional arguments for the SplitIntervals command","required":false,"type":"String"},"tabix_extra_args":{"allow_empty":true,"default":"","help":"Additional arguments for tabix command","required":false,"type":"String"},"vcf2maf_extra_args":{"allow_empty":true,"help":"Additional arguments for the vcf2maf command","required":false,"type":"String"},"work_dir":{"help":"Absolute path to output directory","mode":"w","required":false,"type":"Path"}}

If the above changes are surprising, stop and determine what happened.

If the above changes are expected, there are two ways to fix this:

  1. Automatically: Post a comment starting with "/fix-tests" (without the quotes) and I will update the tests for you (you must review my work afterwards).
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sorelfitzgibbon commented 6 months ago

/fix-tests

github-actions[bot] commented 6 months ago

Bleep bloop, I am a robot.

I have updated all of the failing tests for you with fea4113b15cbaa0dfda57c46637fd329b06bbb02. You must review my work before merging this pull request!

sorelfitzgibbon commented 6 months ago

@dependabot recreate