6 commits

Author	SHA1	Message	Date
fbdtemme	4619d012e5	Add cram support to Allelecounter module (#1013) ... * Add CRAM support to allelecounter * Update meta.yml * Rename bam,bai to input,input_index * Apply suggestions from code review * Fix reference to renamed variable Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>	2021-11-02 17:00:25 +01:00
Harshil Patel	49da864287	Update versions key in meta.yml for all modules (#787)	2021-10-03 08:20:26 +01:00
Harshil Patel	7b3315591a	Remove def software lines and emit versions channel as plural (#780) ... * Remove def software line * Replace version with versions in emit statement * Fix default software names	2021-10-01 14:04:56 +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	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