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Author	SHA1	Message	Date
SusiJo	0708f343de	Merge branch 'master' into cnvkit_bam	2022-05-24 07:49:51 +02:00
SusiJo	361b3a458b	Merge pull request #1686 from SusiJo/cnvkit/antitarget ... Added module cnvkit/antitarget	2022-05-24 07:48:55 +02:00
SusiJo	1451d62be4	rm md5sums for empty files	2022-05-24 07:38:53 +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
Matthias De Smet	91f9a0711d	Merge pull request #1683 from matthdsm/update/picard ... picard: make reference sequence optional	2022-05-23 20:06:11 +02:00
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	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	51bd58809d	Merge pull request #1676 from FriederikeHanssen/gatk_filter ... Gatk filtervarianttranches	2022-05-23 15:54:57 +02:00
FriederikeHanssen	754afa9ff3	Merge branch 'master' into gatk_filter	2022-05-23 15:37:44 +02:00
Rike	e34dcdd8bc	add brackets to contains	2022-05-23 13:19:42 +02:00
Rike	dc6ad1bff6	add brackets to contains	2022-05-23 13:07:08 +02:00
Rike	093e3aafdd	contains	2022-05-23 13:04:49 +02:00
Rike	a8de9fd085	test path update	2022-05-23 12:53:36 +02:00
Rike	3af61cfbbc	fix input cardinality for index	2022-05-23 12:26:12 +02:00
Rike	175ea9b7f9	fix version	2022-05-23 12:15:33 +02:00
Rike	a8dac59c50	md5sum not consistent	2022-05-23 12:10:50 +02:00
Rike	2f36a44f61	nf-core create-test-yml	2022-05-23 12:00:31 +02:00
SusiJo	fd31f64266	Merge branch 'master' into cnvkit_bam	2022-05-23 11:31:56 +02:00
Rike	cd60b4c6eb	add in testdata paths	2022-05-22 13:35:35 +02:00
Rike	5d72500d60	remove variables used for test data generation, add tbi	2022-05-22 13:34:56 +02:00
Rike	520dd06ca3	add new testdata	2022-05-22 13:25:39 +02:00
Matthias De Smet	e13fbf423e	fix tests (again)	2022-05-22 06:54:09 +02:00
Matthias De Smet	cbceee9621	fix tests	2022-05-22 06:51:27 +02:00
Matthias De Smet	3a2de0cf6f	update test for wgsmetrics	2022-05-22 06:49:31 +02:00
Matthias De Smet	c390385cf5	revert wgsmetrics'	2022-05-22 06:44:17 +02:00
Matthias De Smet	4da143ce62	add tests	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	7a83ca3070	Merge pull request #1682 from mahesh-panchal/mash_screen ... Add mash screen	2022-05-20 16:47:36 +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	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