8 commits

Author	SHA1	Message	Date
Moritz E. Beber	879d42c5e2	Refactor adapterremoval (#1491) ... * refactor: insert .fastq file extensions * style: insert whitespace * refactor: create paired output * refactor: rename settings from log Requested by @jfy133 * tests: correct expected output * fix: remove settings option due to default * chore: rename output patterns * refactor: omit paired files in single-end * refactor: rename output to settings	2022-04-04 21:40:35 +02:00
Edmund Miller	f080015754	Prettier (#1405) ... * style: Add prettier config files * build: Add prettier vscode extension * ci: Replace markdownlint and yamllint with prettier * style: Run prettier * style: Use indent of 2 for markdown as well https://github.com/nf-core/tools/pull/1470#issuecomment-1071028358 * style: Fix indent * style: Let editorconfig take over tab widths * style: yaml => yml * ci: Run prettier once Co-authored-by: Phil Ewels <phil.ewels@scilifelab.se> Co-authored-by: Phil Ewels <phil.ewels@scilifelab.se>	2022-03-18 14:27:50 +01:00
James A. Fellows Yates	625098a408	Adapterremoval glob fix (#1391) ... * fix: remove left-over unnecessary code * Partial fix for AR module output declarations * Remove `def` for prefix so useable in output block * Fix tests * Add adapterlist support * Fix tests after addition of adapter list	2022-03-14 07:32:21 +01:00
James A. Fellows Yates	0816df1e8b	Fix: removes hardcoded flags and 'custom' file output for AdapterRemoval (#1357) ... * fix: remove left-over unnecessary code * Removes hardcoded flags and more explicit output * Fix test md5	2022-03-03 10:01:39 +01:00
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
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/adapterremoval/meta.yml (Browse further)