nf-core_modules/tests/config/pytest_subworkflows.yml

subworkflows/align_bowtie2:
  - subworkflows/nf-core/align_bowtie2/**
  - tests/subworkflows/nf-core/align_bowtie2/**

subworkflows/bam_stats_samtools:
  - subworkflows/nf-core/bam_stats_samtools/**
  - tests/subworkflows/nf-core/bam_stats_samtools/**

subworkflows/bam_sort_samtools:
  - subworkflows/nf-core/bam_sort_samtools/**
  - tests/subworkflows/nf-core/bam_sort_samtools/**

subworkflows/sra_fastq:
  - subworkflows/nf-core/sra_fastq/**
  - tests/subworkflows/nf-core/sra_fastq/**
Subworkflow Infrastructure (#662) * feat(subworkflows): Add align_bowtie2 subworkflow For testing CI setup * test(align_bowtie2): Add initial list of changes to test * test(align_bowtie2): Add initial test * refactor: Use tags to run subworkflows ci For every underlying module used by workflow and allow the modules pytest-modules definition be the source of truth. * refactor: Use individual directories for subworkflows * docs(align_bowtie2): Add initial meta.yml Copied most of it from the bowtie2/align module. * fix(align_bowtie2): Fix module include paths * test(bam_sort_samtools): Add initial test * ci(bam_sort_samtools): Add modules that trigger the tag * test(bam_stats_samtools): Add initial test * ci(bam_stats_samtools): Add keys to pick up changes * docs(bam_samtools): Add initial meta.yml * test(align_bowtie2): Fix path to subworkflow * test(align_bowtie2): Update entry point * fix(bam_sort_samtools): Update include paths * test(bam_sort_samtools): Fix path * style: Clean up addParams * test(samtools_sort): Add suffix for test * test(align_bowtie2): Add samtools_options for suffix * test(bam_stats_samtools): Update path * test(bam_stats_samtools): Use stats input Otherwise it's just an example of how it's used in the bam_sort_samtools subworkflow * ci(linting): Skip module linting of subworkflows * ci(linting): Clean up startsWith statement * test(bam_stats_samtools): Use single end test data for single end test * test(bam_stats_samtools): Add expected files * test(align_bowtie2): Add paired-end test * test(align_bowtie2): Sort order of output * test(align_bowtie2): Update hashes * docs(align_bowtie2): Fix typo * test(align_bowtie2): Update samtools output names * test(align_bowtie2): Remove md5sums for bam/bai * feat(subworkflows): Add nextflow.configs These can be used for default settings in the future. They can then be included in the conf/modules.config so that the params don't have to be duplicated in the root nextflow.config. * docs(subworkflows): Include modules instead of tools * fix: Update to versions * chore(align_bowtie2): Remove duplicate tag * style: Format yamls * test(subworkflows): Only check versions for modules * chore: Update subworkflows to match rnaseq dev * fix(subworkflows): Update paths * fix(bam_sort_samtools): Fix sort parameters for testing * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * docs: Update TODOs with a message * ci: Try using a matrix for strategy * ci: Try passing an array * Revert "ci: Try passing an array" This reverts commit d3611fcd8332bbb9a8501e8dd299d0a623aaecaa. Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> 2021-10-08 15:02:42 +00:00			`subworkflows/align_bowtie2:`
			`- subworkflows/nf-core/align_bowtie2/**`
			`- tests/subworkflows/nf-core/align_bowtie2/**`

			`subworkflows/bam_stats_samtools:`
			`- subworkflows/nf-core/bam_stats_samtools/**`
			`- tests/subworkflows/nf-core/bam_stats_samtools/**`

			`subworkflows/bam_sort_samtools:`
			`- subworkflows/nf-core/bam_sort_samtools/**`
			`- tests/subworkflows/nf-core/bam_sort_samtools/**`
feat: add sub-workflow for SRA (#836) * feat: add sub-workflow for SRA * Combine prefetch and fasterq-dump into one sub-workflow * tests: add sub-workflow to pytest config 2021-10-14 09:50:31 +00:00
			`subworkflows/sra_fastq:`
			`- subworkflows/nf-core/sra_fastq/**`
			`- tests/subworkflows/nf-core/sra_fastq/**`