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6 commits

Author SHA1 Message Date
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