8 commits

Author	SHA1	Message	Date
Benedetto Polimeni	d5d785b3d8	[samtools] add optional csi output (#2064) ... * [samtools] add optional csi output, when applicable * Remove empty line Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> Co-authored-by: Matthieu Muffato <mm49@sanger.ac.uk>	2022-09-20 21:08:29 +01:00
nvnieuwk	720027275c	small update to samtools/merge (#1896)	2022-07-18 11:37:45 +02:00
Matthias Hörtenhuber	e745e167c1	Fix formatting in yaml files, add yamllint config (#1279) ... * fix yml formatting * allow fastq.gz and fq.gz as file input, add meta.yml and test * fix yaml files * Revert "allow fastq.gz and fq.gz as file input, add meta.yml and test" This reverts commit 34002d7a7a8c7f7bb4600c3377f35c87849f71a4. * prettier magic! * fix comments for yamllint * remove node version number * fix linting errors Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>	2022-02-15 11:15:27 +00:00
FriederikeHanssen	ac1e6df076	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 13:01:05 +02:00
Kevin	3aacd46da2	Backfill software licenses meta (#876) ... * backfilled modules with meta.yml that had no license identifier * harmonized BSD license names * whitespace linting at modules/unzip/meta.yml:12 * harmonized software from US NIH-NCBI/NIST to 'US-Government-Work' * Update modules/bcftools/index/meta.yml `bcftools` is dual-licensed, use associative array to allow for multiple licenses Co-authored-by: Michael L Heuer <heuermh@acm.org> Co-authored-by: Michael L Heuer <heuermh@acm.org>	2021-10-22 15:39:54 -07:00
Harshil Patel	49da864287	Update versions key in meta.yml for all modules (#787)	2021-10-03 08:20:26 +01:00
Gregor Sturm	906577873b	Bulk update modules to use versions.yml (#739) ... * New functions.nf * Convert code to create versions.yml * Update meta.yml * update output channel * Fix more meta.yml * Manually update remaining modules * remove superflous echo * Fix misformatted meta.yml files * Fix yaml, was list instead of dict * fix version for bcftools Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>	2021-09-27 09:41:24 +01:00
Harshil Patel	e937c7950a	Rename software/ directory to modules/ to re-organise module structure (#567) ... * Update README * Rename pytest_software.yml to pytest_modules.yml * Rename main software directory to modules * Remove deprecated modules * Rename tests software to modules * Replace paths for tests in pytest_modules.yml * Replace software with modules in Github Actions * Replace software with modules in main.nf tests * Rename software to modules in test.yml	2021-07-07 10:10:18 +01:00

Renamed from software/samtools/merge/meta.yml (Browse further)