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use underscores in anchors and references (#1080)

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* use underscores in anchors and references

* Dummy change to trigger CI

* use dev branch

* underscore anchor
This commit is contained in:
Robert A. Petit III 2021-11-18 11:09:09 -07:00 committed by GitHub
parent 5b975cc20d
commit f052dc445c
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3 changed files with 31 additions and 32 deletions
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2
.github/workflows/nf-core-linting.yml vendored
View file

@ -60,7 +60,7 @@ jobs:
# FIXME: Remove this when nf-core modules lint stabilizes and install stable release # FIXME: Remove this when nf-core modules lint stabilizes and install stable release
- name: Install nf-core tools development version - name: Install nf-core tools development version
run: python -m pip install --upgrade --force-reinstall git+https://github.com/nf-core/tools.git@subworkflow_hacks run: python -m pip install --upgrade --force-reinstall git+https://github.com/nf-core/tools.git@dev
- name: Install Nextflow - name: Install Nextflow
env: env:

1
subworkflows/nf-core/gatk_create_som_pon/main.nf
View file

@ -1,7 +1,6 @@
// //
// Run GATK mutect2, genomicsdbimport and createsomaticpanelofnormals // Run GATK mutect2, genomicsdbimport and createsomaticpanelofnormals
// //
params.mutect2_options = [args: '--max-mnp-distance 0'] params.mutect2_options = [args: '--max-mnp-distance 0']
params.gendbimport_options = [:] params.gendbimport_options = [:]
params.createsompon_options = [:] params.createsompon_options = [:]

60
tests/config/pytest_modules.yml
View file

@ -474,7 +474,7 @@ gatk4/bedtointervallist:
- modules/gatk4/bedtointervallist/** - modules/gatk4/bedtointervallist/**
- tests/modules/gatk4/bedtointervallist/** - tests/modules/gatk4/bedtointervallist/**
gatk4/calculatecontamination: &gatk4/calculatecontamination gatk4/calculatecontamination: &gatk4_calculatecontamination
- modules/gatk4/calculatecontamination/** - modules/gatk4/calculatecontamination/**
- tests/modules/gatk4/calculatecontamination/** - tests/modules/gatk4/calculatecontamination/**
@ -482,7 +482,7 @@ gatk4/createsequencedictionary:
- modules/gatk4/createsequencedictionary/** - modules/gatk4/createsequencedictionary/**
- tests/modules/gatk4/createsequencedictionary/** - tests/modules/gatk4/createsequencedictionary/**
gatk4/createsomaticpanelofnormals: &gatk4/createsomaticpanelofnormals gatk4/createsomaticpanelofnormals: &gatk4_createsomaticpanelofnormals
- modules/gatk4/createsomaticpanelofnormals/** - modules/gatk4/createsomaticpanelofnormals/**
- tests/modules/gatk4/createsomaticpanelofnormals/** - tests/modules/gatk4/createsomaticpanelofnormals/**
@ -494,11 +494,11 @@ gatk4/fastqtosam:
- modules/gatk4/fastqtosam/** - modules/gatk4/fastqtosam/**
- tests/modules/gatk4/fastqtosam/** - tests/modules/gatk4/fastqtosam/**
gatk4/filtermutectcalls: &gatk4/filtermutectcalls gatk4/filtermutectcalls: &gatk4_filtermutectcalls
- modules/gatk4/filtermutectcalls/** - modules/gatk4/filtermutectcalls/**
- tests/modules/gatk4/filtermutectcalls/** - tests/modules/gatk4/filtermutectcalls/**
gatk4/genomicsdbimport: &gatk4/genomicsdbimport gatk4/genomicsdbimport: &gatk4_genomicsdbimport
- modules/gatk4/genomicsdbimport/** - modules/gatk4/genomicsdbimport/**
- tests/modules/gatk4/genomicsdbimport/** - tests/modules/gatk4/genomicsdbimport/**
@ -506,7 +506,7 @@ gatk4/genotypegvcfs:
- modules/gatk4/genotypegvcfs/** - modules/gatk4/genotypegvcfs/**
- tests/modules/gatk4/genotypegvcfs/** - tests/modules/gatk4/genotypegvcfs/**
gatk4/getpileupsummaries: &gatk4/getpileupsummaries gatk4/getpileupsummaries: &gatk4_getpileupsummaries
- modules/gatk4/getpileupsummaries/** - modules/gatk4/getpileupsummaries/**
- tests/modules/gatk4/getpileupsummaries/** - tests/modules/gatk4/getpileupsummaries/**
@ -522,7 +522,7 @@ gatk4/intervallisttools:
- modules/gatk4/intervallisttools/** - modules/gatk4/intervallisttools/**
- tests/modules/gatk4/intervallisttools/** - tests/modules/gatk4/intervallisttools/**
gatk4/learnreadorientationmodel: &gatk4/learnreadorientationmodel gatk4/learnreadorientationmodel: &gatk4_learnreadorientationmodel
- modules/gatk4/learnreadorientationmodel/** - modules/gatk4/learnreadorientationmodel/**
- tests/modules/gatk4/learnreadorientationmodel/** - tests/modules/gatk4/learnreadorientationmodel/**
@ -538,7 +538,7 @@ gatk4/mergevcfs:
- modules/gatk4/mergevcfs/** - modules/gatk4/mergevcfs/**
- tests/modules/gatk4/mergevcfs/** - tests/modules/gatk4/mergevcfs/**
gatk4/mutect2: &gatk4/mutect2 gatk4/mutect2: &gatk4_mutect2
- modules/gatk4/mutect2/** - modules/gatk4/mutect2/**
- tests/modules/gatk4/mutect2/** - tests/modules/gatk4/mutect2/**
@ -1187,7 +1187,7 @@ samtools/idxstats:
- modules/samtools/idxstats/** - modules/samtools/idxstats/**
- tests/modules/samtools/idxstats/** - tests/modules/samtools/idxstats/**
samtools/index: &samtools/index samtools/index: &samtools_index
- modules/samtools/index/** - modules/samtools/index/**
- tests/modules/samtools/index/** - tests/modules/samtools/index/**
@ -1199,7 +1199,7 @@ samtools/mpileup:
- modules/samtools/mpileup/** - modules/samtools/mpileup/**
- tests/modules/samtools/mpileup/** - tests/modules/samtools/mpileup/**
samtools/sort: &samtools/sort samtools/sort: &samtools_sort
- modules/samtools/sort/** - modules/samtools/sort/**
- tests/modules/samtools/sort/** - tests/modules/samtools/sort/**
@ -1275,11 +1275,11 @@ spatyper:
- modules/spatyper/** - modules/spatyper/**
- tests/modules/spatyper/** - tests/modules/spatyper/**
sratools/fasterqdump: &sratools/fasterqdump sratools/fasterqdump: &sratools_fasterqdump
- modules/sratools/fasterqdump/** - modules/sratools/fasterqdump/**
- tests/modules/sratools/fasterqdump/** - tests/modules/sratools/fasterqdump/**
sratools/prefetch: &sratools/prefetch sratools/prefetch: &sratools_prefetch
- modules/sratools/prefetch/** - modules/sratools/prefetch/**
- tests/modules/sratools/prefetch/** - tests/modules/sratools/prefetch/**
@ -1399,47 +1399,47 @@ yara/mapper:
- modules/yara/mapper/** - modules/yara/mapper/**
- tests/modules/yara/mapper/** - tests/modules/yara/mapper/**
subworkflows/bam_stats_samtools: &subworkflows/bam_stats_samtools subworkflows/bam_stats_samtools: &subworkflows_bam_stats_samtools
- subworkflows/nf-core/bam_stats_samtools/** - subworkflows/nf-core/bam_stats_samtools/**
- tests/subworkflows/nf-core/bam_stats_samtools/** - tests/subworkflows/nf-core/bam_stats_samtools/**
subworkflows/bam_sort_samtools: &subworkflows/bam_sort_samtools subworkflows/bam_sort_samtools: &subworkflows_bam_sort_samtools
- subworkflows/nf-core/bam_sort_samtools/** - subworkflows/nf-core/bam_sort_samtools/**
- tests/subworkflows/nf-core/bam_sort_samtools/** - tests/subworkflows/nf-core/bam_sort_samtools/**
- *samtools/sort - *samtools_sort
- *samtools/index - *samtools_index
- *subworkflows/bam_stats_samtools - *subworkflows_bam_stats_samtools
subworkflows/align_bowtie2: subworkflows/align_bowtie2:
- subworkflows/nf-core/align_bowtie2/** - subworkflows/nf-core/align_bowtie2/**
- tests/subworkflows/nf-core/align_bowtie2/** - tests/subworkflows/nf-core/align_bowtie2/**
- *subworkflows/bam_sort_samtools - *subworkflows_bam_sort_samtools
subworkflows/sra_fastq: subworkflows/sra_fastq:
- subworkflows/nf-core/sra_fastq/** - subworkflows/nf-core/sra_fastq/**
- tests/subworkflows/nf-core/sra_fastq/** - tests/subworkflows/nf-core/sra_fastq/**
- *sratools/fasterqdump - *sratools_fasterqdump
- *sratools/prefetch - *sratools_prefetch
subworkflows/gatk_create_som_pon: subworkflows/gatk_create_som_pon:
- subworkflows/nf-core/gatk_create_som_pon/** - subworkflows/nf-core/gatk_create_som_pon/**
- tests/subworkflows/nf-core/gatk_create_som_pon/** - tests/subworkflows/nf-core/gatk_create_som_pon/**
- *gatk4/genomicsdbimport - *gatk4_genomicsdbimport
- *gatk4/createsomaticpanelofnormals - *gatk4_createsomaticpanelofnormals
subworkflows/gatk_tumor_normal_somatic_variant_calling: subworkflows/gatk_tumor_normal_somatic_variant_calling:
- subworkflows/nf-core/gatk_tumor_normal_somatic_variant_calling/** - subworkflows/nf-core/gatk_tumor_normal_somatic_variant_calling/**
- tests/subworkflows/nf-core/gatk_tumor_normal_somatic_variant_calling/** - tests/subworkflows/nf-core/gatk_tumor_normal_somatic_variant_calling/**
- *gatk4/mutect2 - *gatk4_mutect2
- *gatk4/learnreadorientationmodel - *gatk4_learnreadorientationmodel
- *gatk4/getpileupsummaries - *gatk4_getpileupsummaries
- *gatk4/calculatecontamination - *gatk4_calculatecontamination
- *gatk4/filtermutectcalls - *gatk4_filtermutectcalls
subworkflows/gatk_tumor_only_somatic_variant_calling: subworkflows/gatk_tumor_only_somatic_variant_calling:
- subworkflows/nf-core/gatk_tumor_only_somatic_variant_calling/** - subworkflows/nf-core/gatk_tumor_only_somatic_variant_calling/**
- tests/subworkflows/nf-core/gatk_tumor_only_somatic_variant_calling/** - tests/subworkflows/nf-core/gatk_tumor_only_somatic_variant_calling/**
- *gatk4/mutect2 - *gatk4_mutect2
- *gatk4/getpileupsummaries - *gatk4_getpileupsummaries
- *gatk4/calculatecontamination - *gatk4_calculatecontamination
- *gatk4/filtermutectcalls - *gatk4_filtermutectcalls