1190 commits

Author	SHA1	Message	Date
Gisela Gabernet	5a16cf7bae	Merge branch 'master' into cellranger-7.0.0	2022-06-10 11:19:57 +02:00
Alexander Peltzer	62c4b59d10	Update main.nf	2022-06-10 11:05:59 +02:00
Thiseas C. Lamnidis	9948e9fe21	Merge branch 'master' into sexdeterrmine	2022-06-10 11:03:18 +02:00
Thiseas C. Lamnidis	fe855a1c23	Apply suggestions from code review ... Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>	2022-06-10 11:03:01 +02:00
Alexander Peltzer	cfcd93f3e7	Update Dockerfile	2022-06-10 10:56:13 +02:00
Alexander Peltzer	61d87bb2bc	Update main.nf	2022-06-10 10:54:06 +02:00
Alexander Peltzer	e499abe572	Update main.nf	2022-06-10 10:53:48 +02:00
Alexander Peltzer	8032833e6e	Update main.nf	2022-06-10 10:53:09 +02:00
Alexander Peltzer	e36b79201d	Update Dockerfile	2022-06-10 10:52:13 +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
nvnieuwk	e88a4ff70b	Merge branch 'master' into add-optional-fasta-parameter-to-ensemblvep	2022-06-09 11:54:22 +02:00
Nicolas Vannieuwkerke	5ccf6fbcc9	add optional fasta argument to ensemblvep	2022-06-09 11:45:27 +02:00
SusiJo	cda434611f	fix conda with openjdk 1.8	2022-06-09 10:24:39 +02:00
SusiJo	0204d2374b	Merge remote-tracking branch 'origin/master' into gatk_spark	2022-06-09 09:33:17 +02:00
James A. Fellows Yates	70f7f07a37	Apply suggestions from code review ... Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>	2022-06-09 08:33:37 +02:00
James Fellows Yates	939653a47e	Changes after code review	2022-06-09 08:26:04 +02:00
James Fellows Yates	4d7afa21e2	Add GATK indelrealigner tests	2022-06-08 21:14:08 +02:00
James A. Fellows Yates	1fc0d3de4b	Merge branch 'gatk3-indelrealigner' into upstream-for-indel	2022-06-08 20:30:19 +02:00
James A. Fellows Yates	4a2157e5ab	Merge branch 'master' into gatk-realigntargetcreator	2022-06-08 20:15:02 +02:00
Ramprasad Neethiraj	0b090a6b6d	Merge branch 'master' of https://github.com/nf-core/modules into rhocall	2022-06-08 16:34:34 +02:00
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
Ramprasad Neethiraj	1648d2fcba	add index	2022-06-08 14:36:25 +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
Ramprasad Neethiraj	16e5e6093c	Merge branch 'master' of https://github.com/nf-core/modules into rhocall	2022-06-07 14:45:09 +02:00
Ramprasad Neethiraj	17a4e93142	fix versions.yaml	2022-06-07 14:43:35 +02:00
Ramprasad Neethiraj	65a0fb959f	rhocall	2022-06-07 14:37:03 +02:00
SusiJo	e78ad2f88b	Merge remote-tracking branch 'origin' into gatk_spark	2022-06-07 14:00:26 +02:00
Matthias De Smet	bffd1c562b	Merge branch 'master' into update/multiqc	2022-06-07 13:59:00 +02:00
SusiJo	dbca9e8b36	adjusted prefix + test + authors	2022-06-07 13:58:57 +02:00
Matthias De Smet	e5bf87aec3	possible fix for name collisions	2022-06-07 13:58:27 +02:00