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

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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:
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
Add thread option to samtools modules (#1069) * add thread option to samtools modules * fix tests * fix tests * fix tests * Fix naming to fix tests * cpus-1 to account for mainthread * remove thread in ampliconclip, docu doesn't report this param * add -1 to all other applicable samtools modules * Update samtools version * Update checksums * retrigger GHA after update * Update modules/samtools/fastq/main.nf Co-authored-by: Patrick Hüther <patrick.huether@gmail.com> * Update modules/samtools/fixmate/main.nf Co-authored-by: Patrick Hüther <patrick.huether@gmail.com> * Update modules/samtools/flagstat/main.nf Co-authored-by: Patrick Hüther <patrick.huether@gmail.com> * Update modules/samtools/index/main.nf Co-authored-by: Patrick Hüther <patrick.huether@gmail.com> * Update modules/samtools/merge/main.nf Co-authored-by: Patrick Hüther <patrick.huether@gmail.com> * Update modules/samtools/stats/main.nf Co-authored-by: Patrick Hüther <patrick.huether@gmail.com> * Update modules/samtools/view/main.nf Co-authored-by: Patrick Hüther <patrick.huether@gmail.com> * Fix md5sum fixmate * Fix md5sums * sth funny with the fixmate checksums * more md5sums updates Co-authored-by: Patrick Hüther <patrick.huether@gmail.com>
2021-11-18 21:24:47 +00:00
- samtools
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
Add thread option to samtools modules (#1069) * add thread option to samtools modules * fix tests * fix tests * fix tests * Fix naming to fix tests * cpus-1 to account for mainthread * remove thread in ampliconclip, docu doesn't report this param * add -1 to all other applicable samtools modules * Update samtools version * Update checksums * retrigger GHA after update * Update modules/samtools/fastq/main.nf Co-authored-by: Patrick Hüther <patrick.huether@gmail.com> * Update modules/samtools/fixmate/main.nf Co-authored-by: Patrick Hüther <patrick.huether@gmail.com> * Update modules/samtools/flagstat/main.nf Co-authored-by: Patrick Hüther <patrick.huether@gmail.com> * Update modules/samtools/index/main.nf Co-authored-by: Patrick Hüther <patrick.huether@gmail.com> * Update modules/samtools/merge/main.nf Co-authored-by: Patrick Hüther <patrick.huether@gmail.com> * Update modules/samtools/stats/main.nf Co-authored-by: Patrick Hüther <patrick.huether@gmail.com> * Update modules/samtools/view/main.nf Co-authored-by: Patrick Hüther <patrick.huether@gmail.com> * Fix md5sum fixmate * Fix md5sums * sth funny with the fixmate checksums * more md5sums updates Co-authored-by: Patrick Hüther <patrick.huether@gmail.com>
2021-11-18 21:24:47 +00:00
md5sum: 09146eeecfcae2a84fb8615c86cd8d64
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/stats
Add thread option to samtools modules (#1069) * add thread option to samtools modules * fix tests * fix tests * fix tests * Fix naming to fix tests * cpus-1 to account for mainthread * remove thread in ampliconclip, docu doesn't report this param * add -1 to all other applicable samtools modules * Update samtools version * Update checksums * retrigger GHA after update * Update modules/samtools/fastq/main.nf Co-authored-by: Patrick Hüther <patrick.huether@gmail.com> * Update modules/samtools/fixmate/main.nf Co-authored-by: Patrick Hüther <patrick.huether@gmail.com> * Update modules/samtools/flagstat/main.nf Co-authored-by: Patrick Hüther <patrick.huether@gmail.com> * Update modules/samtools/index/main.nf Co-authored-by: Patrick Hüther <patrick.huether@gmail.com> * Update modules/samtools/merge/main.nf Co-authored-by: Patrick Hüther <patrick.huether@gmail.com> * Update modules/samtools/stats/main.nf Co-authored-by: Patrick Hüther <patrick.huether@gmail.com> * Update modules/samtools/view/main.nf Co-authored-by: Patrick Hüther <patrick.huether@gmail.com> * Fix md5sum fixmate * Fix md5sums * sth funny with the fixmate checksums * more md5sums updates Co-authored-by: Patrick Hüther <patrick.huether@gmail.com>
2021-11-18 21:24:47 +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:
- path: output/samtools/test.paired_end.recalibrated.sorted.cram.stats
Add thread option to samtools modules (#1069) * add thread option to samtools modules * fix tests * fix tests * fix tests * Fix naming to fix tests * cpus-1 to account for mainthread * remove thread in ampliconclip, docu doesn't report this param * add -1 to all other applicable samtools modules * Update samtools version * Update checksums * retrigger GHA after update * Update modules/samtools/fastq/main.nf Co-authored-by: Patrick Hüther <patrick.huether@gmail.com> * Update modules/samtools/fixmate/main.nf Co-authored-by: Patrick Hüther <patrick.huether@gmail.com> * Update modules/samtools/flagstat/main.nf Co-authored-by: Patrick Hüther <patrick.huether@gmail.com> * Update modules/samtools/index/main.nf Co-authored-by: Patrick Hüther <patrick.huether@gmail.com> * Update modules/samtools/merge/main.nf Co-authored-by: Patrick Hüther <patrick.huether@gmail.com> * Update modules/samtools/stats/main.nf Co-authored-by: Patrick Hüther <patrick.huether@gmail.com> * Update modules/samtools/view/main.nf Co-authored-by: Patrick Hüther <patrick.huether@gmail.com> * Fix md5sum fixmate * Fix md5sums * sth funny with the fixmate checksums * more md5sums updates Co-authored-by: Patrick Hüther <patrick.huether@gmail.com>
2021-11-18 21:24:47 +00:00
md5sum: 62377b29c3f6253e37308a28d13a496d
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