3160 commits

This branch

This branch

All branches

Author	SHA1	Message	Date
SusiJo	35e296cd7d	added brackets	2022-05-31 15:35:34 +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
SusiJo	37b543e3e7	changed to tab	2022-05-31 15:29:27 +02:00
SusiJo	810564deca	Merge branch 'master' into gatk_spark	2022-05-31 15:24:58 +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
SusiJo	9ef09e6add	adjusted newlines	2022-05-31 14:54:39 +02:00
SusiJo	205576279f	ran prettier again	2022-05-31 14:50:55 +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
SusiJo	d484aa1906	adjusted tabs	2022-05-31 14:45:23 +02:00
SusiJo	e083bfafa0	ran prettier	2022-05-31 14:38:45 +02:00
SusiJo	1e396d767f	Merge remote-tracking branch 'upstream/master' into gatk_spark	2022-05-31 14:36:14 +02:00
SusiJo	ea526051a4	new test.yml	2022-05-31 14:35:42 +02:00
SusiJo	3117b2973c	added test for metrics	2022-05-31 14:35:29 +02:00
SusiJo	e0e8273f74	adjusted input to use queryname sorted bams	2022-05-31 14:35:18 +02:00
SusiJo	39e34418c9	added metrics as optional output	2022-05-31 14:34:50 +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
James Fellows Yates	7ffe98ac8b	Add gatk/indelrealigner	2022-05-30 21:12:21 +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
Matthias De Smet	63db63757c	bump picard versions	2022-05-30 10:15:40 +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
jtangrot	05e4e2cdde	Add idcutoff as input	2022-05-26 20:16:45 +02:00
Sateesh Peri	ead3679829	Merge branch 'master' into rp3-add-snippy	2022-05-26 03:04:19 -04:00
Harshil Patel	f89b76afa4	Merge pull request #1701 from matthdsm/update/mosdepth ... Mosdepth: add all remaining outputs	2022-05-25 19:46:37 +01:00
Harshil Patel	72a31b76eb	Update main.nf	2022-05-25 19:42:15 +01:00
Harshil Patel	241a1de035	Update main.nf	2022-05-25 19:38:12 +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	038fced07e	Merge pull request #1698 from mahesh-panchal/mash_screen_patch ... Patch mash screen	2022-05-25 17:00:01 +02:00
Mahesh Binzer-Panchal	3d532405a5	Merge branch 'master' into mash_screen_patch	2022-05-25 16:51:42 +02:00
SusiJo	b34e5ea6bf	rm unnecessary spark_user	2022-05-25 16:38:48 +02:00
SusiJo	1400f2e683	fixed tests - mixed chr21 + chr22	2022-05-25 16:38:30 +02:00
SusiJo	dd6d838cd7	override userEmulation	2022-05-25 16:37:44 +02:00