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  -c ./tests/modules/samtools/stats/nextflow.config
  tags:
    - samtools/stats
    - samtools
  files:
    - path: output/samtools/test.stats
      md5sum: 5e6fa3805f6d6b330262456746709239

- name: samtools stats test_samtools_stats_cram
  command: nextflow run ./tests/modules/samtools/stats -entry test_samtools_stats_cram -c ./tests/config/nextflow.config  -c ./tests/modules/samtools/stats/nextflow.config
  tags:
    - samtools/stats
    - samtools
  files:
    - path: output/samtools/test.stats
      md5sum: 916a8e5bfd97a53f806e5a14565631bb
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`
samtools/stats: use prefix for outputs (#1788) * use prefix in flagstat * use prefix in idxstats * use prefix in stats * update test.yml 2022-06-16 11:42:01 +00:00			`command: nextflow run ./tests/modules/samtools/stats -entry test_samtools_stats -c ./tests/config/nextflow.config -c ./tests/modules/samtools/stats/nextflow.config`
Restructure tests to run individually for each module 2021-02-03 16:02:58 +00:00			`tags:`
samtools/stats: use prefix for outputs (#1788) * use prefix in flagstat * use prefix in idxstats * use prefix in stats * update test.yml 2022-06-16 11:42:01 +00:00			`- samtools/stats`
fix samtools stats thread usage (#1975) * fix samtools stats thread usage * fix checksums 2022-08-29 10:05:47 +00:00			`- samtools`
Restructure tests to run individually for each module 2021-02-03 16:02:58 +00:00			`files:`
samtools/stats: use prefix for outputs (#1788) * use prefix in flagstat * use prefix in idxstats * use prefix in stats * update test.yml 2022-06-16 11:42:01 +00:00			`- path: output/samtools/test.stats`
fix samtools stats thread usage (#1975) * fix samtools stats thread usage * fix checksums 2022-08-29 10:05:47 +00:00			`md5sum: 5e6fa3805f6d6b330262456746709239`
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`
samtools/stats: use prefix for outputs (#1788) * use prefix in flagstat * use prefix in idxstats * use prefix in stats * update test.yml 2022-06-16 11:42:01 +00:00			`command: nextflow run ./tests/modules/samtools/stats -entry test_samtools_stats_cram -c ./tests/config/nextflow.config -c ./tests/modules/samtools/stats/nextflow.config`
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			`tags:`
samtools/stats: use prefix for outputs (#1788) * use prefix in flagstat * use prefix in idxstats * use prefix in stats * update test.yml 2022-06-16 11:42:01 +00:00			`- samtools/stats`
fix samtools stats thread usage (#1975) * fix samtools stats thread usage * fix checksums 2022-08-29 10:05:47 +00:00			`- samtools`
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			`files:`
samtools/stats: use prefix for outputs (#1788) * use prefix in flagstat * use prefix in idxstats * use prefix in stats * update test.yml 2022-06-16 11:42:01 +00:00			`- path: output/samtools/test.stats`
fix samtools stats thread usage (#1975) * fix samtools stats thread usage * fix checksums 2022-08-29 10:05:47 +00:00			`md5sum: 916a8e5bfd97a53f806e5a14565631bb`