7 commits

Author	SHA1	Message	Date
Matthias De Smet	cdbe648400	align	2022-05-16 14:44:32 +02:00
Matthias De Smet	2cca156fed	linting	2022-05-16 14:42:34 +02:00
Matthias De Smet	af69ea749d	add module: biobambam/bammerge	2022-05-16 14:39:58 +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
Matthias De Smet	797ce3254e	Update: biobambam/bammarkduplicates2 to v2.0.183 (#1493) ... * bump version, remove md5sums from test * re-add md5sums	2022-04-05 11:06:46 +02:00
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
Matthieu Muffato	04e82ec61a	First version of the biobambam/bammarkduplicates2 module (#1247) ... * First version of the biobambam/bammarkduplicates2 module * Fixed the path of versions.yml * Regenerated the checksums as the previous files were generated with a single core * Added the `when:` block, as per #1261 Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>	2022-02-14 16:30:48 +00:00