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