5 commits

Author	SHA1	Message	Date
Harshil Patel	b932210f27	Fix flash and cat/fastq modules (#759) ... * Fix version commands: round 3 * Fix seqkit/split2 modules * Fix flash and cat/fastq modules * Remove md5sums on gz files	2021-09-28 21:14:11 +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	1d6f47ce54	Refactor cat/cat module (#723) ... * Refactor cat/cat module * Change gzip terminology	2021-09-21 11:17:00 +01:00
Daniel Lundin	b32c46c6a2	CAT CAT (#722) ... * bbmap/align done * Tests for single end and prebuilt index * Write bam file directly * Forgot to use all cpus for bbmap * Test md5sums * Added pigz support * Update modules/bbmap/align/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * process_medium and fastq * cat/cat module * Remove filter from CAT_CAT Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>	2021-09-20 21:02:22 +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