128 commits

Author	SHA1	Message	Date
FriederikeHanssen	1ac223ad43	GATK/Getpileupsummaries: If no intervals use variants instead (#1787) ... If no intervals use variants instead	2022-06-16 15:00:01 +02:00
Maxime U. Garcia	878a5a8093	Merge branch 'master' into update_spark	2022-06-09 15:49:31 +02:00
Rike	6a4732ef3b	similar issues arise with bqsrspark, also use broadinstitute container	2022-06-09 15:29:00 +02:00
Rike	8e8f4c9c51	remove singulairty container	2022-06-09 15:16:11 +02:00
nvnieuwk	873215c8ae	Update modules/gatk4/reblockgvcf/main.nf ... Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>	2022-06-09 15:11:18 +02:00
Rike	89a6a03e38	fix container tag	2022-06-09 15:09:19 +02:00
Nicolas Vannieuwkerke	81fff7384d	small fix and typo	2022-06-09 15:08:02 +02:00
Rike	b9e397ff15	use broadinstitute container	2022-06-09 15:06:46 +02:00
nvnieuwk	bf73b6d376	Merge branch 'master' into new-module-gatk4/reblockgvcf	2022-06-09 14:57:20 +02:00
Nicolas Vannieuwkerke	fe9e4ece00	new module gatk4/reblockgvcf	2022-06-09 14:56:55 +02:00
Rike	ef5b0dd977	gatk4 version update to 4.2.6.1	2022-06-09 14:54:19 +02:00
SusiJo	cda434611f	fix conda with openjdk 1.8	2022-06-09 10:24:39 +02:00
SusiJo	e78ad2f88b	Merge remote-tracking branch 'origin' into gatk_spark	2022-06-07 14:00:26 +02:00
SusiJo	dbca9e8b36	adjusted prefix + test + authors	2022-06-07 13:58:57 +02:00
Nicolas Vannieuwkerke	4c7ef30fb6	changed to label to medium	2022-06-07 12:17:14 +02:00
Nicolas Vannieuwkerke	771425e7a0	add threads to calibratedragstrmodel	2022-06-07 12:11:18 +02:00
SusiJo	e2bb56608c	change prefix output	2022-06-03 13:50:45 +02:00
SusiJo	230224700e	change prefix	2022-06-03 13:20:45 +02:00
SusiJo	1db7771ea9	Merge branch 'nf-core:master' into gatk_spark	2022-06-03 13:17:35 +02:00
SusiJo	1b93cde9ff	Merge branch 'master' into gatk_spark	2022-06-02 16:24:39 +02:00
Nicolas Vannieuwkerke	f3c0107fa2	added optional to intervals	2022-06-02 16:24:03 +02:00
SusiJo	efc1e1bb71	rm line ... Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>	2022-06-02 16:23:18 +02:00
SusiJo	44daa5d687	update prefix ... Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>	2022-06-02 16:23:09 +02:00
Nicolas Vannieuwkerke	b4b1f3b81d	add intervals to calibratedragstrmodel	2022-06-02 16:20:12 +02:00
Nicolas Vannieuwkerke	e53d091a6d	added dragstr model to haplotypecaller	2022-06-02 14:08:09 +02:00
nvnieuwk	3a49b82863	Update modules/gatk4/calibratedragstrmodel/main.nf ... Co-authored-by: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>	2022-06-02 13:39:44 +02:00
Nicolas Vannieuwkerke	d3874bbae9	linting	2022-06-02 13:22:55 +02:00
Nicolas Vannieuwkerke	2a45d42868	added the calibratedragstrmodel module	2022-06-02 13:17:06 +02:00
Nicolas Vannieuwkerke	114a54c8d5	spaces fix	2022-06-01 09:22:09 +02:00
nvnieuwk	5b74a179c3	Update modules/gatk4/composestrtablefile/main.nf ... Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>	2022-06-01 09:14:08 +02:00
nvnieuwk	e4f51d6f59	Merge branch 'master' into new-module-gatk4/ComposeSTRTableFile	2022-06-01 08:59:19 +02:00
asp8200	4199a05aeb	Removing redundant empty line	2022-05-31 15:34:34 +00:00
Nicolas Vannieuwkerke	80366924fd	added gatk4/composestrtablefile	2022-05-31 16:08:13 +02:00
Anders Sune Pedersen	5513d095f5	Adding tbi-files to the output from GATK4_MERGEVCFS. #1709	2022-05-31 15:37:26 +02:00
SusiJo	39e34418c9	added metrics as optional output	2022-05-31 14:34:50 +02:00
SusiJo	b34e5ea6bf	rm unnecessary spark_user	2022-05-25 16:38:48 +02:00
Rike	175ea9b7f9	fix version	2022-05-23 12:15:33 +02:00
Rike	5d72500d60	remove variables used for test data generation, add tbi	2022-05-22 13:34:56 +02:00
Rike	bb3e64647b	Merge remote-tracking branch 'origin/master' into gatk_filter	2022-05-18 15:52:47 +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
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
Praveen Raj S	df2620cfc7	Merge branch 'master' into process_lable_markdup	2022-05-16 15:53:26 +02:00
Rike	ba14355891	revert markduplciatespark changes	2022-05-16 09:54:40 +02:00
FriederikeHanssen	8b4d021189	Merge branch 'master' into gatk_426	2022-05-16 09:50:13 +02:00
Nicolas Vannieuwkerke	6427eeeca0	added tmp-dir + alignment correction	2022-05-13 14:35:22 +02:00
Nicolas Vannieuwkerke	1c2a991429	fixed memory warning	2022-05-13 14:25:53 +02:00