nf-core_modules/tests/modules/samtools/stats/test.yml

- name: samtools stats test_samtools_stats
  command: nextflow run tests/modules/samtools/stats -entry test_samtools_stats -c tests/config/nextflow.config
  tags:
    - samtools
    - samtools/stats
  files:
    - path: output/samtools/test.paired_end.sorted.bam.stats
      md5sum: a7f36cf11fd3bf97e0a0ae29c0627296

- name: samtools stats test_samtools_stats_cram
  command: nextflow run tests/modules/samtools/stats -entry test_samtools_stats_cram -c tests/config/nextflow.config
  tags:
    - samtools
    - samtools/stats
  files:
    - path: output/samtools/test.paired_end.recalibrated.sorted.cram.stats
      md5sum: bd55a1da30028403f4b66dacf7a2a20e
Update to allow cram + update needed to use the gatk4 modules in sarek (#976) * Make samtools/merge cram compliant * samtools/stats cram compliance * update yml file * samtools/view to deal with crams * Update tests to make sure cram works * also fix tmp dir and min mem in one go * basequalityrecal test for cram + min mem + tmpdir * update haplotypecaller for sarek * update haplotype yml * update markdup to allow multiple bams, take out params to be passed with options.args * remove TODO statement * Remove variable md5sum * add emtpy input to stats module in subworkflows * subworkflows seem to work now on my side * Apply code review Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se> * replace bam with input to be more inclusive * rename everywhere * rename input * remove variable checksum Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se> 2021-10-29 11:01:05 +00:00			`- name: samtools stats test_samtools_stats`
			`command: nextflow run tests/modules/samtools/stats -entry test_samtools_stats -c tests/config/nextflow.config`
Restructure tests to run individually for each module 2021-02-03 16:02:58 +00:00			`tags:`
			`- samtools`
Lint modules ci (#389) * ci: Add modules lint step Moved it ahead of the nextflow install so ideally it'll fail before we bother doing any more setup * ci: _ => / * Update tests/config/pytest_software.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> 2021-04-08 08:10:52 +00:00			`- samtools/stats`
Restructure tests to run individually for each module 2021-02-03 16:02:58 +00:00			`files:`
Update to allow cram + update needed to use the gatk4 modules in sarek (#976) * Make samtools/merge cram compliant * samtools/stats cram compliance * update yml file * samtools/view to deal with crams * Update tests to make sure cram works * also fix tmp dir and min mem in one go * basequalityrecal test for cram + min mem + tmpdir * update haplotypecaller for sarek * update haplotype yml * update markdup to allow multiple bams, take out params to be passed with options.args * remove TODO statement * Remove variable md5sum * add emtpy input to stats module in subworkflows * subworkflows seem to work now on my side * Apply code review Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se> * replace bam with input to be more inclusive * rename everywhere * rename input * remove variable checksum Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se> 2021-10-29 11:01:05 +00:00			`- path: output/samtools/test.paired_end.sorted.bam.stats`
nf-core modules bump-versions for all modules (#630) * Add blacklist of modules that shouldn't be updated to .nf-core.yml * nf-core modules bump-versions for all modules * Remove TODO statements identified by linting * Fix md5sums for failing tests * Fix more tests 2021-07-28 08:10:44 +00:00			`md5sum: a7f36cf11fd3bf97e0a0ae29c0627296`
Update to allow cram + update needed to use the gatk4 modules in sarek (#976) * Make samtools/merge cram compliant * samtools/stats cram compliance * update yml file * samtools/view to deal with crams * Update tests to make sure cram works * also fix tmp dir and min mem in one go * basequalityrecal test for cram + min mem + tmpdir * update haplotypecaller for sarek * update haplotype yml * update markdup to allow multiple bams, take out params to be passed with options.args * remove TODO statement * Remove variable md5sum * add emtpy input to stats module in subworkflows * subworkflows seem to work now on my side * Apply code review Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se> * replace bam with input to be more inclusive * rename everywhere * rename input * remove variable checksum Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se> 2021-10-29 11:01:05 +00:00
			`- name: samtools stats test_samtools_stats_cram`
			`command: nextflow run tests/modules/samtools/stats -entry test_samtools_stats_cram -c tests/config/nextflow.config`
			`tags:`
			`- samtools`
			`- samtools/stats`
			`files:`
			`- path: output/samtools/test.paired_end.recalibrated.sorted.cram.stats`
			`md5sum: bd55a1da30028403f4b66dacf7a2a20e`