1065 commits

Author	SHA1	Message	Date
SusiJo	7742661784	Merge remote-tracking branch 'upstream/master' into cnvkit_bam	2022-06-02 10:51:43 +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
Nicolas Vannieuwkerke	114a54c8d5	spaces fix	2022-06-01 09:22:09 +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	615cb0722f	Merge branch 'master' into fix-filtlong	2022-05-31 20:25:16 +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	80366924fd	added gatk4/composestrtablefile	2022-05-31 16:08:13 +02:00
James Fellows Yates	089f761f0b	Actually add the changes	2022-05-31 15:49:57 +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	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	0b895871d7	Merge branch 'master' into fix-filtlong	2022-05-31 14:49:44 +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
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	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	fb6c7bca3d	Bump container version for STAR to 2.7.10a	2022-05-27 11:35:04 +01:00
Harshil Patel	72a31b76eb	Update main.nf	2022-05-25 19:42:15 +01:00
Matthias De Smet	bc7002b0c9	Merge branch 'master' into update/mosdepth	2022-05-25 19:20:45 +02:00
Matthias De Smet	72ff2732e3	add all remaining outputs to mosdepth	2022-05-25 19:19:39 +02:00
Mahesh Binzer-Panchal	3d532405a5	Merge branch 'master' into mash_screen_patch	2022-05-25 16:51:42 +02:00
Mahesh Binzer-Panchal	c452f56289	Patch mash screen	2022-05-25 12:29:14 +00:00
Jill V. Hagey, PhD	b1dd1d8a52	Merge branch 'nf-core:master' into gamma-update	2022-05-24 19:28:06 -04:00
Mahesh Binzer-Panchal	3d51956b88	Merge branch 'master' into kat_hist	2022-05-24 23:10:13 +02:00
jvhagey	b8aaea7429	updating paths in test.yml	2022-05-24 16:27:00 -04:00
jvhagey	f1fc7fc38e	adding upzip	2022-05-24 15:15:07 -04:00
Ramprasad Neethiraj	fe90615f57	Merge branch 'rhocall' of github.com:genomic-medicine-sweden/modules into rhocall	2022-05-24 16:17:59 +02:00
Ramprasad Neethiraj	b0dba3ee75	update description	2022-05-24 16:17:15 +02:00
Ramprasad Neethiraj	c91947f8a1	Merge branch 'master' into rhocall	2022-05-24 16:07:55 +02:00
Mahesh Binzer-Panchal	9a5d6a815b	Merge branch 'master' into kat_hist	2022-05-24 15:46:12 +02:00
SusiJo	3077e4d34c	Merge branch 'master' into cnvkit/reference	2022-05-24 15:00:29 +02:00
SusiJo	8208140d21	missing meta.id changed	2022-05-24 14:59:52 +02:00
SusiJo	6b425735b9	Merge remote-tracking branch 'origin/master' into cnvkit/reference	2022-05-24 14:20:55 +02:00
SusiJo	749edce069	add prefix	2022-05-24 14:20:19 +02:00
Mahesh Binzer-Panchal	c8ffecfe86	Merge branch 'master' into kat_hist	2022-05-24 13:57:45 +02:00
Matthias De Smet	c51c047b2e	Merge branch 'master' into update/mosdepth	2022-05-24 13:50:22 +02:00
Matthias De Smet	a2a8e09762	Update modules/mosdepth/main.nf ... Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>	2022-05-24 13:45:52 +02:00
Mahesh Binzer-Panchal	afb5f226e6	Merge branch 'master' into kat_hist	2022-05-24 13:06:31 +02:00
Matthias De Smet	858cbe80c6	add must fail test	2022-05-24 12:43:49 +02:00
Matthias De Smet	7e777c6626	add error is is provided twice	2022-05-24 12:25:31 +02:00