1449 commits

Author	SHA1	Message	Date
Ramprasad Neethiraj	c91947f8a1	Merge branch 'master' into rhocall	2022-05-24 16:07:55 +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
Matthias De Smet	8381a5e5dd	add window test	2022-05-24 14:43:40 +02:00
Matthias De Smet	5bc2d419a9	fix fail test	2022-05-24 13:23:00 +02:00
Matthias De Smet	858cbe80c6	add must fail test	2022-05-24 12:43:49 +02:00
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
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	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
SusiJo	33a72367c6	Merge branch 'nf-core:master' into cnvkit_reference	2022-05-24 07:30:29 +02:00
Harshil Patel	a3e70777ad	Fix Conda tests	2022-05-23 22:39:12 +01:00
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	8fec7ae321	added new testdata path	2022-05-23 19:01:46 +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	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
Ramprasad Neethiraj	9fb327fec7	Merge branch 'master' of https://github.com/nf-core/modules into rhocall	2022-05-23 13:06:00 +02:00
Rike	093e3aafdd	contains	2022-05-23 13:04:49 +02:00
Ramprasad Neethiraj	06a3bff201	fix lint error	2022-05-23 12:59:48 +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	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	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	4da143ce62	add tests	2022-05-22 06:44:17 +02:00
Ramprasad Neethiraj	995bf88327	add stub	2022-05-20 17:10:09 +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	00077c36c8	removed unnecessary fasta for tumor_only_bam	2022-05-20 13:06:16 +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
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