7 commits

Author	SHA1	Message	Date
James A. Fellows Yates	90aef30f43	Set process label to process_single for modules with no task.cpus usage (#2076) ... * Set process label to `process_single` for modules with no `task.cpus` usage * Fix tests of 'borked' modules * prettier * More modules are single-threaded and can use process_single * Adding process_single to hmmer/esl* modules * Fix failing tests * Prettier Co-authored-by: Matthieu Muffato <mm49@sanger.ac.uk> Co-authored-by: Daniel Lundin <erik.rikard.daniel@gmail.com>	2022-09-19 11:54:47 +02:00
James A. Fellows Yates	15c7190e22	Deeparg singularity container fix 2 (#1406) ... * fix: remove left-over unnecessary code * Switch to more portable solution for singularity container issue by using bind paths * Fix input collision of dummy files * Repalce dummy with which bash * Remove dummy usage from tests * Apply suggestions from code review * Fix singularity typo	2022-03-18 16:21:55 +01:00
James A. Fellows Yates	f469045a95	Fix DeepARG depenency issue with singularity containers (#1397) ... * fix: remove left-over unnecessary code * Adds --fakeroot option for singularity usage with DeepARG as workaround for broken conda dependency * Update modules/deeparg/downloaddata/main.nf Co-authored-by: Moritz E. Beber <midnighter@posteo.net> * Update modules/deeparg/predict/main.nf Co-authored-by: Moritz E. Beber <midnighter@posteo.net> * Apply suggestions from code review * Update main.nf * Update main.nf * Update main.nf * Update main.nf * Go back to original logic Co-authored-by: Moritz E. Beber <midnighter@posteo.net>	2022-03-17 13:08:51 +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
Mahesh Binzer-Panchal	e20e57f90b	Add when: block (#1261)	2022-02-04 09:53:32 +01:00
James A. Fellows Yates	fc1e694e6e	fix: remove left-over unnecessary code (#1235)	2022-01-27 09:38:06 +01:00
James A. Fellows Yates	c3bacb9fdd	Add deeparg (#1234) ... * Add deeparg download data * Tweak downloaddata test.yml * Add deeparg tests * Apply suggestions from code review * Fix output file paths in test * Fix tests again md5sum to string	2022-01-26 15:19:16 +01:00