3 commits

Author	SHA1	Message	Date
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
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
Sébastien Guizard	79d38a306b	New module: isoseq3/refine (#748) ... * 📦 NEW: Add isoseq3/refine module * 👌 IMPROVE: Add some pacbio test files * 🐛 FIX: Add Pacbio index to test_data.config * 👌 IMPROVE: Re add 10000 data test * 👌 IMPROVE: Add parallelization * 🐛 FIX: Correct Typo * 👌 IMPROVE: Add some pbindex * 🐛 FIX: Add pbi extension to files * 👌 IMPROVE: The module accept one channel (primers moved into the first channel) * 👌 IMPROVE: Assign a value channel to primers input Improve workflow code readability * 👌 IMPROVE: Update to the version of templates * 👌 IMPROVE: Update module to last template version * 👌 IMPROVE: Remove pbi from input files * 👌 IMPROVE: Update test file * 👌 IMPROVE: Final version of test datasets config * 👌 IMPROVE: Remove useless index + Fix Typos * 👌 IMPROVE: Fill contains args * 📦 NEW: Add isoseq3/refine module * 👌 IMPROVE: Add parallelization * 🐛 FIX: Correct Typo * 👌 IMPROVE: Add some pacbio test files * 🐛 FIX: Add Pacbio index to test_data.config * 👌 IMPROVE: Re add 10000 data test * 👌 IMPROVE: Add some pbindex * 🐛 FIX: Add pbi extension to files * 👌 IMPROVE: The module accept one channel (primers moved into the first channel) * 👌 IMPROVE: Assign a value channel to primers input Improve workflow code readability * 👌 IMPROVE: Update to the version of templates * 👌 IMPROVE: Update module to last template version * 👌 IMPROVE: Remove pbi from input files * 👌 IMPROVE: Update test file * 👌 IMPROVE: Final version of test datasets config * 👌 IMPROVE: Remove useless index + Fix Typos * 👌 IMPROVE: Fill contains args * 👌 IMPROVE: Add one channel per output file * 👌 IMPROVE: Minor updates * 👌 IMPROVE: Minors Update - Remove TODO from test.yml - Remove useless piece of code * 📦 NEW: Add isoseq3/refine module * 👌 IMPROVE: Add parallelization * 🐛 FIX: Correct Typo * 👌 IMPROVE: Add some pacbio test files * 🐛 FIX: Add Pacbio index to test_data.config * 👌 IMPROVE: Re add 10000 data test * 👌 IMPROVE: Add some pbindex * 🐛 FIX: Add pbi extension to files * 👌 IMPROVE: The module accept one channel (primers moved into the first channel) * 👌 IMPROVE: Assign a value channel to primers input Improve workflow code readability * 👌 IMPROVE: Update to the version of templates * 👌 IMPROVE: Update module to last template version * 👌 IMPROVE: Remove pbi from input files * 👌 IMPROVE: Update test file * 👌 IMPROVE: Fill contains args * 📦 NEW: Add isoseq3/refine module * 👌 IMPROVE: Add parallelization * 🐛 FIX: Correct Typo * 👌 IMPROVE: Add some pacbio test files * 🐛 FIX: Add Pacbio index to test_data.config * 👌 IMPROVE: Re add 10000 data test * 👌 IMPROVE: Add some pbindex * 🐛 FIX: Add pbi extension to files * 👌 IMPROVE: The module accept one channel (primers moved into the first channel) * 👌 IMPROVE: Assign a value channel to primers input Improve workflow code readability * 👌 IMPROVE: Update to the version of templates * 👌 IMPROVE: Update module to last template version * 👌 IMPROVE: Remove pbi from input files * 👌 IMPROVE: Update test file * 👌 IMPROVE: Add one channel per output file * 👌 IMPROVE: Minor updates * 👌 IMPROVE: Minors Update - Remove TODO from test.yml - Remove useless piece of code * 🐛 FIX: Remove unwanted files * 🐛 FIX: Protect \ * 🐛 FIX: Remove test files * Apply suggestions from code review * Apply suggestions from code review * Update tests/modules/isoseq3/refine/test.yml Co-authored-by: Gregor Sturm <mail@gregor-sturm.de> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>	2021-10-06 11:13:48 +01:00