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Author	SHA1	Message	Date
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	00077c36c8	removed unnecessary fasta for tumor_only_bam	2022-05-20 13:06:16 +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	3d57caa683	added test & corrected cram input	2022-05-20 09:13:27 +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	c8ccfe3710	Merge pull request #1675 from FriederikeHanssen/gatk_cnnscore ... Gatk cnnscore	2022-05-18 15:44:52 +02:00
FriederikeHanssen	44e9cf56fa	Merge branch 'master' into gatk_cnnscore	2022-05-18 15:32:36 +02:00
Rike	11d514cd30	Merge remote-tracking branch 'origin/gatk_cnnscore' into gatk_cnnscore	2022-05-18 14:33:15 +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	9f8d6cbdd5	Merge pull request #1616 from jianhong/motus_profile ... Motus profile	2022-05-18 12:26:31 +01:00
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
FriederikeHanssen	fdf1bec20b	Merge branch 'master' into gatk_cnnscore	2022-05-17 23:07:09 +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	afa0f2a995	update test	2022-05-17 22:53:41 +02:00
Rike	265fd882ca	update test	2022-05-17 19:44:48 +02:00
Rike	5f63904a50	update test	2022-05-17 19:37:18 +02:00
Rike	05611cf27c	update pytest	2022-05-17 19:11:05 +02:00
Rike	e0fcbb428d	Add CNNScoreVariants	2022-05-17 19:09:46 +02:00
Matthias De Smet	856a8712f8	Merge pull request #1667 from matthdsm/biobambam/bammerge	2022-05-17 17:09:06 +02:00
Jose Espinosa-Carrasco	3614c19206	Merge branch 'master' into biobambam/bammerge	2022-05-17 15:07:37 +02:00
Jose Espinosa-Carrasco	fbf20c1e36	Merge pull request #1673 from nvnieuwk/new-module-bedtools/split ... new module: bedtools split	2022-05-17 14:45:07 +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	c5627e0274	fix config	2022-05-17 09:09:19 +02:00
Matthias De Smet	743e95c61b	fix config	2022-05-17 09:01:02 +02:00
Matthias De Smet	d3ddc2221a	Merge branch 'master' into biobambam/bammerge	2022-05-17 08:26:28 +02:00
Matthias De Smet	53c4a2d1cd	Merge pull request #1657 from sysbiocoder/hmtnote ... Hmtnote	2022-05-17 08:21:32 +02:00
Matthias De Smet	6be91ce82d	fix optional output detection	2022-05-17 08:20:47 +02:00
Subazini TK	79c2c529fc	Merge branch 'master' into hmtnote	2022-05-17 08:05:47 +02:00
JIANHONG OU	671bacb6df	Merge branch 'master' into motus_profile	2022-05-16 17:34:49 -04:00
Matthias De Smet	d0db186e84	Merge branch 'master' into biobambam/bammerge	2022-05-16 20:52:48 +02:00
Matthias De Smet	a79b9adeee	address review comments	2022-05-16 20:51:39 +02:00
Gregor Sturm	9036b90eb6	Merge pull request #1178 from veitveit/maxquant ... New module: Maxquant	2022-05-16 19:32:23 +02:00
Subazini TK	00204fa82b	Update main.nf	2022-05-16 15:20:15 +00:00
Subazini TK	252fcb17c4	Update main.nf	2022-05-16 15:20:15 +00:00
Subazini TK	cb21fa0c96	Update main.nf	2022-05-16 15:20:15 +00:00
Subazini TK	cbae48d06d	Update nextflow.config	2022-05-16 15:20:15 +00:00
Subazini TK	541f403963	Update main.nf	2022-05-16 15:20:15 +00:00