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ci(bam_sort_samtools): Depend on paths-filter instead of pytest-workflow

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Co-authored-by: Harshil Patel <drpatelhh@gmail.com>
Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
This commit is contained in:
Edmund Miller 2021-10-27 11:42:34 -05:00
parent 04cf48b663
commit 59818c2b86
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GPG key ID: BD387FF7BC10AA9D
2 changed files with 17 additions and 14 deletions
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7
tests/config/pytest_modules.yml
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@ -1163,7 +1163,7 @@ samtools/idxstats:
- modules/samtools/idxstats/** - modules/samtools/idxstats/**
- tests/modules/samtools/idxstats/** - tests/modules/samtools/idxstats/**
samtools/index: samtools/index: &samtools/index
- modules/samtools/index/** - modules/samtools/index/**
- tests/modules/samtools/index/** - tests/modules/samtools/index/**
@ -1175,7 +1175,7 @@ samtools/mpileup:
- modules/samtools/mpileup/** - modules/samtools/mpileup/**
- tests/modules/samtools/mpileup/** - tests/modules/samtools/mpileup/**
samtools/sort: samtools/sort: &samtools/sort
- modules/samtools/sort/** - modules/samtools/sort/**
- tests/modules/samtools/sort/** - tests/modules/samtools/sort/**
@ -1386,6 +1386,9 @@ subworkflows/bam_stats_samtools: &subworkflows/bam_stats_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/index
- *subworkflows/bam_stats_samtools
subworkflows/sra_fastq: subworkflows/sra_fastq:
- subworkflows/nf-core/sra_fastq/** - subworkflows/nf-core/sra_fastq/**

24
tests/subworkflows/nf-core/bam_sort_samtools/test.yml
View file

@ -4,12 +4,12 @@
- subworkflows/bam_sort_samtools - subworkflows/bam_sort_samtools
- subworkflows/bam_stats_samtools - subworkflows/bam_stats_samtools
# Modules # Modules
- samtools # - samtools
- samtools/index # - samtools/index
- samtools/sort # - samtools/sort
- samtools/stats # - samtools/stats
- samtools/idxstats # - samtools/idxstats
- samtools/flagstat # - samtools/flagstat
files: files:
- path: ./output/samtools/test.sorted.bam - path: ./output/samtools/test.sorted.bam
md5sum: e4c77897d6824ce4df486d1b100618af md5sum: e4c77897d6824ce4df486d1b100618af
@ -28,12 +28,12 @@
- subworkflows/bam_sort_samtools - subworkflows/bam_sort_samtools
- subworkflows/bam_stats_samtools - subworkflows/bam_stats_samtools
# Modules # Modules
- samtools # - samtools
- samtools/index # - samtools/index
- samtools/sort # - samtools/sort
- samtools/stats # - samtools/stats
- samtools/idxstats # - samtools/idxstats
- samtools/flagstat # - samtools/flagstat
files: files:
- path: ./output/samtools/test.sorted.bam - path: ./output/samtools/test.sorted.bam
md5sum: bbb2db225f140e69a4ac577f74ccc90f md5sum: bbb2db225f140e69a4ac577f74ccc90f