1111 commits

Author	SHA1	Message	Date
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
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	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
Sateesh Peri	ead3679829	Merge branch 'master' into rp3-add-snippy	2022-05-26 03:04:19 -04:00
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
Matthias De Smet	b5850fd471	add stub	2022-05-24 12:16:03 +02:00
Harshil Patel	393f23274d	Merge branch 'master' into cnvkit/reference	2022-05-24 11:14:50 +01:00
Harshil Patel	29a4f112be	Update main.nf	2022-05-24 11:14:32 +01:00
Matthias De Smet	01fb8851c3	mosdept: cram compatiblility	2022-05-24 11:47:58 +02:00
Harshil Patel	ec141dba08	Merge branch 'master' into umitools	2022-05-24 09:23:20 +01:00
SusiJo	5db94ea0ee	changed tag of module	2022-05-24 10:17:41 +02:00
Ramprasad Neethiraj	b4982ff6e3	Merge branch 'master' into rhocall	2022-05-24 09:41:30 +02:00
SusiJo	0f0d555f96	Merge branch 'master' into cnvkit_reference	2022-05-24 08:03:44 +02:00
SusiJo	0708f343de	Merge branch 'master' into cnvkit_bam	2022-05-24 07:49:51 +02:00
SusiJo	50128b0c86	Merge branch 'master' into cnvkit_reference	2022-05-24 07:49:44 +02:00
SusiJo	63c038ad68	Merge branch 'nf-core:master' into cnvkit_bam	2022-05-24 07:37:24 +02:00
SusiJo	b3e2f70651	Merge branch 'master' into cnvkit/antitarget	2022-05-24 07:36:07 +02:00
SusiJo	33a72367c6	Merge branch 'nf-core:master' into cnvkit_reference	2022-05-24 07:30:29 +02:00
Harshil Patel	84f02a08a5	Update umitools/dedup module to make --output-stats optional	2022-05-23 22:31:09 +01:00
Sateesh Peri	da0ead705e	Merge branch 'master' into update/picard	2022-05-23 13:38:18 -04:00
SusiJo	58c5ec2f4e	rm line ... Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>	2022-05-23 18:53:28 +02:00
SusiJo	86b5951c14	rm line ... Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>	2022-05-23 18:48:30 +02:00
SusiJo	24905e26e2	rm line ... Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>	2022-05-23 18:48:13 +02:00
SusiJo	ddb964a4bf	rm line ... Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>	2022-05-23 18:48:04 +02:00
SusiJo	bbee9e3c3b	add new module cnvkit/reference	2022-05-23 18:35:50 +02:00
SusiJo	5d5eacee63	Merge branch 'nf-core:master' into cnvkit/antitarget	2022-05-23 16:52:33 +02:00
SusiJo	4f9d672e55	added new module cnvkit/antitarget	2022-05-23 16:52:06 +02:00
FriederikeHanssen	754afa9ff3	Merge branch 'master' into gatk_filter	2022-05-23 15:37:44 +02:00
Ramprasad Neethiraj	9fb327fec7	Merge branch 'master' of https://github.com/nf-core/modules into rhocall	2022-05-23 13:06:00 +02:00
Rike	175ea9b7f9	fix version	2022-05-23 12:15:33 +02:00
SusiJo	fd31f64266	Merge branch 'master' into cnvkit_bam	2022-05-23 11:31:56 +02:00
Mahesh Binzer-Panchal	e06fb752c3	Merge branch 'master' into kat_hist	2022-05-23 08:52:13 +02:00
Rike	5d72500d60	remove variables used for test data generation, add tbi	2022-05-22 13:34:56 +02:00
Matthias De Smet	c390385cf5	revert wgsmetrics'	2022-05-22 06:44:17 +02:00
Matthias De Smet	d6a0238cd1	Merge branch 'master' into update/picard	2022-05-21 08:34:33 +02:00
Matthias De Smet	a5a6973fcf	picard: make reference sequence optional	2022-05-21 08:33:49 +02:00
Ramprasad Neethiraj	635edc0022	fix typo	2022-05-20 17:07:42 +02:00
Ramprasad Neethiraj	2542c9d176	add tests	2022-05-20 16:46:19 +02:00
Mahesh Binzer-Panchal	2926ec0abb	Add mash screen	2022-05-20 13:23:11 +00:00
Ramprasad Neethiraj	c70b169f61	create modules	2022-05-20 13:34:54 +02:00
SusiJo	9096be5464	improve readability	2022-05-20 13:29:49 +02:00
SusiJo	bdf222649d	remove unnecessary if statement	2022-05-20 13:25:57 +02:00
SusiJo	153c900d0e	refine comment ... Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>	2022-05-20 13:08:38 +02:00
SusiJo	2e5aa0dbb4	refine comment ... Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>	2022-05-20 13:08:26 +02:00
SusiJo	3b3921cfa3	refine comment ... Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>	2022-05-20 13:07:57 +02:00
SusiJo	f392c4bed5	removed params section & added description fasta	2022-05-20 13:05:43 +02:00
SusiJo	129270d7bc	adjusted conda env & singularity container	2022-05-20 10:37:46 +02:00
SusiJo	dd2f48810a	Merge branch 'nf-core:master' into cnvkit_bam	2022-05-20 09:14:21 +02:00
SusiJo	5a1297cc7d	added optional pdf/png outputs	2022-05-20 09:12:47 +02:00
SusiJo	064712c4ea	added cram_bam conversion & tumor_only check	2022-05-20 09:11:45 +02:00
Rike	bb3e64647b	Merge remote-tracking branch 'origin/master' into gatk_filter	2022-05-18 15:52:47 +02:00
FriederikeHanssen	44e9cf56fa	Merge branch 'master' into gatk_cnnscore	2022-05-18 15:32:36 +02:00
Rike	e8221cf98e	Merge remote-tracking branch 'origin' into gatk_cnnscore	2022-05-18 14:27:25 +02:00
Rike	10840a0562	Conda not suported	2022-05-18 14:26:21 +02:00
James A. Fellows Yates	965fabdd54	Merge branch 'master' into motus_profile	2022-05-18 11:25:48 +01:00
Rike	5ae757121f	Add indices and meta	2022-05-17 23:38:26 +02:00
Rike	05837a011d	Add comment	2022-05-17 23:06:52 +02:00
Rike	15fba1dd7c	add filter variant tranches	2022-05-17 23:01:24 +02:00
Rike	e0fcbb428d	Add CNNScoreVariants	2022-05-17 19:09:46 +02:00
Jose Espinosa-Carrasco	3614c19206	Merge branch 'master' into biobambam/bammerge	2022-05-17 15:07:37 +02:00
Nicolas Vannieuwkerke	6342f5b099	added bedtools split	2022-05-17 14:24:32 +02:00
Matthias De Smet	f48790a728	replace regex with fixed extensions	2022-05-17 09:54:06 +02:00
Matthias De Smet	94733a85c0	Update modules/biobambam/bammerge/main.nf ... Co-authored-by: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se>	2022-05-17 09:46:19 +02:00