nf-core_modules

1490 commits 30 branches 0 tags 142 MiB

Author	SHA1	Message	Date
James A. Fellows Yates	e971f538a9	Module new version reporting fixes (#753 ) * Specify more guidelines on input channels * Linting * Updates based on code review * Update README.md * Fix broken sentence * Fix IQ tree * Fix picard markdup and merge sam * Fix plink/vcf version * Fix plink version output * Fix prokka version command * Fix pydamage * Try fixing markduplicates * Fix snpEff * Fix vcftools version * Fix pydamage and filtersamreads test run * Fix MarkDuplicates tests * Add missing unsorted checks * Remove MD5 sym due to stochasicity in BAM file	2021-09-28 10:51:19 +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
Mei Wu	b2a6f5409e	modify markduplicates module (#681 ) * tested * updated meta config and test config	2021-09-15 11:02:28 +02:00
Harshil Patel	c5235a983d	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 09:10:44 +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/picard/markduplicates/main.nf (Browse further)

5 commits