1106 commits

Author	SHA1	Message	Date
Taniguti	3be549534d	Apply suggestions from code review ... Co-authored-by: Anders Jemt <jemten@users.noreply.github.com>	2022-06-07 14:09:04 -03:00
Taniguti	a2e2d50494	Merge branch 'master' into haplocheck	2022-06-07 08:16:22 -03:00
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
James A. Fellows Yates	d2b240a17a	Merge branch 'master' into gatk-unifiedgenotyper	2022-06-03 21:24:09 +02:00
James A. Fellows Yates	e827a042ce	Update modules/gatk/unifiedgenotyper/main.nf ... Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>	2022-06-03 21:24:03 +02:00
Robert A. Petit III	d7cec801b2	Update main.nf	2022-06-03 13:05:43 -06:00
Robert A. Petit III	24ca2ed464	Merge branch 'master' into rp3-add-snippy	2022-06-03 13:01:05 -06:00
Matthias De Smet	cf9d62fc83	Merge branch 'master' into bump/picard	2022-06-02 22:09:42 +02:00
James Fellows Yates	a565d9072a	Add GATK UnifiedGenotyper	2022-06-02 21:39:39 +02:00
James Fellows Yates	a14855dbe8	Start meta	2022-06-02 21:22:21 +02:00
James Fellows Yates	544b62df45	Star work on GATK UG	2022-06-02 21:11:17 +02:00
Nicolas Vannieuwkerke	b028e57588	Merge branch 'add-intervals-to-calibratedragstrmodel' of github.com:nvnieuwk/modules into add-intervals-to-calibratedragstrmodel	2022-06-02 16:24:06 +02:00
Nicolas Vannieuwkerke	f3c0107fa2	added optional to intervals	2022-06-02 16:24:03 +02:00
nvnieuwk	897de827ee	Merge branch 'master' into add-intervals-to-calibratedragstrmodel	2022-06-02 16:20:41 +02:00
Nicolas Vannieuwkerke	b4b1f3b81d	add intervals to calibratedragstrmodel	2022-06-02 16:20:12 +02:00
MaxUlysse	b623ff5d27	fix comments	2022-06-02 16:11:45 +02:00
MaxUlysse	bc0f52bcd3	fix cache version	2022-06-02 16:11:11 +02:00
MaxUlysse	046fa39582	update VEP version + cache	2022-06-02 16:09:09 +02:00
Nicolas Vannieuwkerke	e53d091a6d	added dragstr model to haplotypecaller	2022-06-02 14:08:09 +02:00
Matthias De Smet	db0dc81b81	Merge branch 'master' into bump/picard	2022-06-02 13:49:03 +02:00
nvnieuwk	a339f9818a	Merge branch 'master' into new-module-gatk4/CalibrateDragstrModel	2022-06-02 13:42:56 +02:00
nvnieuwk	4b430e8ece	Merge branch 'master' into new-module-gatk4/CalibrateDragstrModel	2022-06-02 13:41:20 +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
Matthias De Smet	f58771c47f	Merge branch 'master' into update/untar	2022-06-02 13:38:53 +02:00
Nicolas Vannieuwkerke	631bf7749a	Merge branch 'new-module-gatk4/CalibrateDragstrModel' of github.com:nvnieuwk/modules into new-module-gatk4/CalibrateDragstrModel	2022-06-02 13:22:57 +02:00
Nicolas Vannieuwkerke	d3874bbae9	linting	2022-06-02 13:22:55 +02:00
nvnieuwk	eadab8e002	Merge branch 'master' into new-module-gatk4/CalibrateDragstrModel	2022-06-02 13:18:36 +02:00
Nicolas Vannieuwkerke	2a45d42868	added the calibratedragstrmodel module	2022-06-02 13:17:06 +02:00
SusiJo	2f3ddc90fb	added fasta_fai as input + changed if statements	2022-06-02 12:57:50 +02:00
Matthias De Smet	45f3795670	Merge branch 'master' into bump/picard	2022-06-02 11:33:26 +02:00
Matthias De Smet	51be617b1c	fix untar output dir	2022-06-02 11:09:55 +02:00
SusiJo	7742661784	Merge remote-tracking branch 'upstream/master' into cnvkit_bam	2022-06-02 10:51:43 +02:00
SusiJo	a21cfb666e	changed container + add cram2bam conversion	2022-06-02 10:38:05 +02:00
SusiJo	9fc9be3e7b	Merge remote-tracking branch 'origin/master' into cnvkit_bam	2022-06-01 17:35:47 +02:00
SusiJo	f6953b5147	adjust cnvkit/batch for germline mode	2022-06-01 17:35:02 +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
James A. Fellows Yates	615cb0722f	Merge branch 'master' into fix-filtlong	2022-05-31 20:25:16 +02:00
FriederikeHanssen	19037ed8f4	Merge branch 'master' into get_tbi_files_from_gatk4_mergevcfs	2022-05-31 17:42:27 +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
James Fellows Yates	089f761f0b	Actually add the changes	2022-05-31 15:49:57 +02:00
Anders Sune Pedersen	5513d095f5	Adding tbi-files to the output from GATK4_MERGEVCFS. #1709	2022-05-31 15:37:26 +02:00
nvnieuwk	a6c7635b73	Merge branch 'master' into add-tbi-to-bcftools-concat	2022-05-31 15:20:03 +02:00
Nicolas Vannieuwkerke	51b0a6e4f3	Added optional input of index files to bcftools/concat	2022-05-31 15:15:58 +02:00
James A. Fellows Yates	0b895871d7	Merge branch 'master' into fix-filtlong	2022-05-31 14:49:44 +02:00
James Fellows Yates	723852bf3d	Fixes running without shortreads, and also ensures all tests produce non-empty fastq.gz files	2022-05-31 13:38:18 +02:00
Sébastien Guizard	a3ae526521	Merge branch 'master' into bamtools/convert/remove_TODO	2022-05-30 17:36:36 +01:00