996 commits

Author	SHA1	Message	Date
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	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
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
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
Mahesh Binzer-Panchal	2926ec0abb	Add mash screen	2022-05-20 13:23:11 +00:00
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
Matthias De Smet	d3ddc2221a	Merge branch 'master' into biobambam/bammerge	2022-05-17 08:26:28 +02:00
Matthias De Smet	6be91ce82d	fix optional output detection	2022-05-17 08:20:47 +02:00