1122 commits

Author	SHA1	Message	Date
Ramprasad Neethiraj	3cabdfac20	Merge branch 'master' into update_roh	2022-06-08 15:04:34 +02:00
Ramprasad Neethiraj	c079ee2025	fix test	2022-06-08 14:48:16 +02:00
Matthias De Smet	e5f8924fab	Update modules/multiqc/main.nf ... Co-authored-by: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se>	2022-06-08 14:41:10 +02:00
Ramprasad Neethiraj	ea4dc866e0	add index	2022-06-08 14:38:55 +02:00
Matthias De Smet	7b018acabb	Update modules/multiqc/main.nf ... Co-authored-by: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se>	2022-06-08 14:36:13 +02:00
Matthias De Smet	100b3f244c	Apply suggestions from code review ... Co-authored-by: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se>	2022-06-08 14:24:55 +02:00
Matthias De Smet	71e3056813	Merge branch 'master' into update/multiqc	2022-06-08 14:03:26 +02:00
Matthias De Smet	f1e33ca6e0	update mqc command	2022-06-08 14:02:04 +02:00
Matthias De Smet	439d2a9e67	update mqc inputs	2022-06-08 13:48:27 +02:00
MaxUlysse	07eff4346f	fix path to symbolic links	2022-06-08 11:46:45 +02:00
Maxime U. Garcia	4935bb98cb	Apply suggestions from code review ... Co-authored-by: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se>	2022-06-08 11:38:02 +02:00
Maxime U. Garcia	7230bf2174	Merge branch 'master' into update_tiddit	2022-06-08 11:16:01 +02:00
Matthias De Smet	d196552e06	update input	2022-06-07 16:33:17 +02:00
Matthias De Smet	bffd1c562b	Merge branch 'master' into update/multiqc	2022-06-07 13:59:00 +02:00
Matthias De Smet	e5bf87aec3	possible fix for name collisions	2022-06-07 13:58:27 +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
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
MaxUlysse	97e66015ca	add test + fix issues	2022-06-03 15:51:02 +02:00
MaxUlysse	f9ac4e28e9	cover all use cases	2022-06-03 15:37:10 +02:00
MaxUlysse	f1a5cc07db	restructure tiddit/sv + test (just one for now)	2022-06-03 13:00:29 +02:00
MaxUlysse	40996cdbe1	update tiddit/cov + more tests	2022-06-03 12:07:16 +02:00
MaxUlysse	36ffd4fbf7	Merge remote-tracking branch 'upstream/master' into update_tiddit	2022-06-03 11:38:33 +02:00
Rike	2c9e2f5e73	Update TIDDIT to 3.0.0	2022-06-03 10:52:50 +02:00
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