millironx/nf-core_modules
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3 commits

Author SHA1 Message Date
Matthias De Smet
6b9a6a5b29
bamsormadup: add extra test case, fix single file input (#1905) 2022-07-19 13:52:37 +02:00
Matthias De Smet
035e418369
Biobambam/bamsormadup: Fix name collision (#1900) 
* Fix name collision

Add stageAs to avoid name collisions

* fix version check

* fix test
 2022-07-18 15:43:02 +02:00
Matthias De Smet
dc95e67e15
New tool: biobambam/bamsormadup (#1478) 
* add bamsormadup

* fix yaml

* add test.yml

* Update tests/modules/biobambam/bamsormadup/test.yml

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* test meta.yaml: remove md5sums

* Tool bamsormadup:
- add (optional) reference input
- add bam index ouput
- add cram output option
- make metrics output: more general

* fix input and output formats

* update input file description

* drop sam output, goes against nf-core regs; add input check for cram files

* fix typo

* Update modules/biobambam/bamsormadup/main.nf

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* improve ref fasta name

* fix if else shorthand

* fix syntax error

* kind of fix tests

* set fixed suffix for metrics file to keep it in line with picard and bammarkduplicates2

* fix command line

* update test.yml

* add support for multiple input bams

* Update modules/biobambam/bamsormadup/meta.yml

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* Update modules/biobambam/bamsormadup/meta.yml

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* Update tests/modules/biobambam/bamsormadup/test.yml

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
 2022-04-06 08:18:23 +02:00