2899 commits

This branch

This branch

All branches

Author	SHA1	Message	Date
SusiJo	2f3ddc90fb	added fasta_fai as input + changed if statements	2022-06-02 12:57:50 +02:00
SusiJo	7742661784	Merge remote-tracking branch 'upstream/master' into cnvkit_bam	2022-06-02 10:51:43 +02:00
SusiJo	3294def3fd	Merge pull request #1722 from SusiJo/deeptools_samtools ... Adjust deeptools/bamcoverage with new mulled container	2022-06-02 10:50:05 +02:00
SusiJo	a21cfb666e	changed container + add cram2bam conversion	2022-06-02 10:38:05 +02:00
SusiJo	9fc9be3e7b	Merge remote-tracking branch 'origin/master' into cnvkit_bam	2022-06-01 17:35:47 +02:00
SusiJo	f6953b5147	adjust cnvkit/batch for germline mode	2022-06-01 17:35:02 +02:00
nvnieuwk	95e8afe627	Merge pull request #1714 from nvnieuwk/new-module-gatk4/ComposeSTRTableFile ... added gatk4/composestrtablefile	2022-06-01 09:33:08 +02:00
Nicolas Vannieuwkerke	114a54c8d5	spaces fix	2022-06-01 09:22:09 +02:00
Nicolas Vannieuwkerke	8470f3cb7e	linting	2022-06-01 09:20:20 +02:00
Nicolas Vannieuwkerke	d4f3df4677	Updated the test	2022-06-01 09:17:05 +02:00
nvnieuwk	5b74a179c3	Update modules/gatk4/composestrtablefile/main.nf ... Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>	2022-06-01 09:14:08 +02:00
nvnieuwk	e4f51d6f59	Merge branch 'master' into new-module-gatk4/ComposeSTRTableFile	2022-06-01 08:59:19 +02:00
James A. Fellows Yates	33af85697b	Merge pull request #1713 from jfy133/fix-filtlong ... Fix filtlong to remove hardcoded output names	2022-05-31 20:50:21 +02:00
James A. Fellows Yates	615cb0722f	Merge branch 'master' into fix-filtlong	2022-05-31 20:25:16 +02:00
James Fellows Yates	df22cd80df	Fix config for tests	2022-05-31 20:07:52 +02:00
FriederikeHanssen	fba7edb652	Merge pull request #1716 from asp8200/get_tbi_files_from_gatk4_mergevcfs ... Get tbi-files from gatk4 mergevcfs	2022-05-31 17:55:06 +02:00
FriederikeHanssen	19037ed8f4	Merge branch 'master' into get_tbi_files_from_gatk4_mergevcfs	2022-05-31 17:42:27 +02:00
asp8200	4199a05aeb	Removing redundant empty line	2022-05-31 15:34:34 +00:00
Nicolas Vannieuwkerke	1166fb5150	prettier	2022-05-31 16:13:38 +02:00
Nicolas Vannieuwkerke	ec41ea6082	fix test.yml	2022-05-31 16:12:05 +02:00
Nicolas Vannieuwkerke	80366924fd	added gatk4/composestrtablefile	2022-05-31 16:08:13 +02:00
asp8200	98bb45cf4e	Updating test for gatk4/mergevcfs	2022-05-31 13:59:56 +00:00
James Fellows Yates	089f761f0b	Actually add the changes	2022-05-31 15:49:57 +02:00
James A. Fellows Yates	edc9e83a7d	Merge branch 'master' into fix-filtlong	2022-05-31 15:47:39 +02:00
James Fellows Yates	3e20ca7e9a	Don't hardcode forced output names	2022-05-31 15:46:28 +02:00
Anders Sune Pedersen	5513d095f5	Adding tbi-files to the output from GATK4_MERGEVCFS. #1709	2022-05-31 15:37:26 +02:00
nvnieuwk	22a90dbd0f	Merge pull request #1711 from nvnieuwk/add-tbi-to-bcftools-concat ... Added optional input of index files to bcftools/concat	2022-05-31 15:33:10 +02:00
nvnieuwk	a6c7635b73	Merge branch 'master' into add-tbi-to-bcftools-concat	2022-05-31 15:20:03 +02:00
Nicolas Vannieuwkerke	51b0a6e4f3	Added optional input of index files to bcftools/concat	2022-05-31 15:15:58 +02:00
James A. Fellows Yates	94dd8f63df	Merge pull request #1710 from jfy133/fix-filtlong ... Fix filtlong - makes running without shortreads work correctly, and also ensures all tests produce …	2022-05-31 14:54:54 +02:00
James A. Fellows Yates	0b895871d7	Merge branch 'master' into fix-filtlong	2022-05-31 14:49:44 +02:00
James Fellows Yates	430def06fa	Switch from md5sum to string due to conda flakiness	2022-05-31 14:45:41 +02:00
James A. Fellows Yates	667a0bc24c	Merge pull request #1708 from sguizard/bamtools/convert/remove_TODO ... 👌 IMPROVE: Remove last TODO	2022-05-31 13:41:41 +02:00
James Fellows Yates	723852bf3d	Fixes running without shortreads, and also ensures all tests produce non-empty fastq.gz files	2022-05-31 13:38:18 +02:00
Sébastien Guizard	a3ae526521	Merge branch 'master' into bamtools/convert/remove_TODO	2022-05-30 17:36:36 +01:00
Sebastien Guizard	d463cd5dd6	👌 IMPROVE: Remove last TODO	2022-05-30 17:26:51 +01:00
Jeanette Tångrot	3bb32b2def	Merge pull request #1705 from jtangrot/vsearch_usearch_global ... Vsearch usearch global	2022-05-30 14:28:01 +02:00
jtangrot	6ae405c5da	prettier	2022-05-30 13:35:12 +02:00
jtangrot	6aac5c2c40	Update test	2022-05-30 13:30:27 +02:00
jtangrot	5f0d75bb37	Merge branch 'vsearch_usearch_global' of https://github.com/jtangrot/nf-core_modules into vsearch_usearch_global	2022-05-30 13:05:00 +02:00
Jeanette Tångrot	69e00b55d3	Update modules/vsearch/usearchglobal/main.nf ... Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com>	2022-05-30 13:03:45 +02:00
jtangrot	c67c15f243	Make input tuple	2022-05-30 13:01:06 +02:00
jtangrot	2e16c90fce	Fix whitespace	2022-05-30 09:57:05 +02:00
jtangrot	5132b004c7	Merge branch 'vsearch_usearch_global' of https://github.com/jtangrot/nf-core_modules into vsearch_usearch_global	2022-05-30 08:55:33 +02:00
jtangrot	01d86439f5	Add idcutoff as input	2022-05-30 08:50:27 +02:00
jtangrot	589ce2d73a	Add options for output file type	2022-05-30 08:50:27 +02:00
jtangrot	1c99ffd876	Add vserach usearch_global	2022-05-30 08:50:27 +02:00
Harshil Patel	b86d792055	Merge pull request #1703 from drpatelh/star ... Bump container version for STAR to 2.7.10a	2022-05-27 12:29:59 +01:00
Harshil Patel	ad578cafcc	Fix tests	2022-05-27 12:14:10 +01:00
Harshil Patel	fb6c7bca3d	Bump container version for STAR to 2.7.10a	2022-05-27 11:35:04 +01:00