millironx/nf-core_modules
1
0
Fork 0
mirror of https://github.com/MillironX/nf-core_modules.git synced 2024-09-21 15:52:05 +00:00
Code Issues Releases Packages Activity
1478 commits 30 branches 0 tags 142 MiB
Commit graph

8 commits

Author SHA1 Message Date
Mei Wu
b2a6f5409e
modify markduplicates module (#681) 
* tested

* updated meta config and test config
 2021-09-15 11:02:28 +02:00
Harshil Patel
c5235a983d
nf-core modules bump-versions for all modules (#630) 
* Add blacklist of modules that shouldn't be updated to .nf-core.yml

* nf-core modules bump-versions for all modules

* Remove TODO statements identified by linting

* Fix md5sums for failing tests

* Fix more tests
 2021-07-28 09:10:44 +01:00
James A. Fellows Yates
553f51d6bf
fix: picard filtersamreads input (#610) 
* Move readlist into same input channel as bam

* Update test reflecting input restructuring

* Update tests/modules/picard/filtersamreads/main.nf

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

* fix test

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
 2021-07-22 11:19:51 +01:00
James A. Fellows Yates
3cc43838e1
module: picard filtersamreads (#602) 
* Start work filtersamreads

* Refactored to allow optional input

* Use proper readlist test data

* Remove typo

* Fix if else condition

* Remove debugging code

* Fix container URLs

* Add required input specification meta

* Cleanup

* Apply suggestions from code review

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

* Fix suffixing

* Additional formatting tweaks

* Update modules/picard/filtersamreads/main.nf

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

* Update modules/picard/filtersamreads/meta.yml

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
 2021-07-21 15:22:19 +01:00
James A. Fellows Yates
2d26b037a1
(another) fix: picard sortsam (#606) 
* Add picard/sortsam module

* Fix container links

* Changes after code review

* Input meta in the right place

* Correct output file suffix

* Define only `bam` in output tuple

* Correct output meta

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
 2021-07-21 15:51:33 +02:00
James A. Fellows Yates
a0019d4175
fix: picard sortsam (#605) 
* Add picard/sortsam module

* Fix container links

* Changes after code review

* Input meta in the right place

* Correct output file suffix

* Define only `bam` in output tuple
 2021-07-21 14:34:21 +01:00
James A. Fellows Yates
1a26d48104
module: picard sortsam (#603) 
* Add picard/sortsam module

* Fix container links

* Changes after code review

* Input meta in the right place
 2021-07-21 13:48:07 +02:00
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