1686 commits

Author	SHA1	Message	Date
Mahesh Binzer-Panchal	f8bd7902d9	Update Git SHA messagre	2022-06-10 11:01:40 +00:00
Mahesh Binzer-Panchal	25c742dc69	Commit suggestions from code review	2022-06-10 10:56:56 +00:00
jasmezz	088b5b14f6	Merge branch 'r-ampir' of github.com:jasmezz/modules into r-ampir	2022-06-10 12:54:47 +02:00
jasmezz	39388abc04	Add file name collision check + TSV output	2022-06-10 12:54:39 +02:00
Mahesh Binzer-Panchal	6a1cbce0f5	Update tests/test_versions_yml.py ... Co-authored-by: Fabian Egli <fabianegli@users.noreply.github.com>	2022-06-10 12:54:08 +02:00
Mahesh Binzer-Panchal	e75dd10667	Merge branch 'master' into allow_git_sha_versions	2022-06-10 12:53:50 +02:00
Alexander Peltzer	a0747b1405	Remove empty file md5sum	2022-06-10 11:53:28 +02:00
Alexander Peltzer	63f47551a8	Fix empty test having md5sum	2022-06-10 11:52:30 +02:00
Alexander Peltzer	1fbe69cfcc	Updated and fixed tests	2022-06-10 11:46:23 +02:00
Mahesh Binzer-Panchal	0479544e02	Allow Git commit SHA's as version numbers	2022-06-10 09:46:14 +00:00
Alexander Peltzer	8dfe8b795f	Merge remote-tracking branch 'refs/remotes/origin/cellranger-7.0.0' into cellranger-7.0.0	2022-06-10 11:23:15 +02:00
Alexander Peltzer	4928dfad34	Trying to fix tests	2022-06-10 11:22:45 +02:00
Alexander Peltzer	570a43ba4c	Fix tests	2022-06-10 11:21:03 +02:00
Thiseas C. Lamnidis	9948e9fe21	Merge branch 'master' into sexdeterrmine	2022-06-10 11:03:18 +02:00
James A. Fellows Yates	c9db677a45	Merge branch 'master' into r-ampir	2022-06-09 19:28:37 +02:00
jasmezz	5841f11edb	Replace MD5 with contains check	2022-06-09 18:15:27 +02:00
jasmezz	ecf1d146ab	Add full user options for AMPir	2022-06-09 16:59:00 +02:00
Maxime U. Garcia	878a5a8093	Merge branch 'master' into update_spark	2022-06-09 15:49:31 +02:00
Rike	30262d1fdd	remove variable checksum	2022-06-09 15:44:12 +02:00
Rike	a5583143c4	update checksum	2022-06-09 15:38:28 +02:00
jasmezz	ba53e09b64	Implement suggestions from code review	2022-06-09 15:37:35 +02:00
Rike	95633c6853	update checksum	2022-06-09 15:30:47 +02:00
Nicolas Vannieuwkerke	c50df9ad04	fix test.yml	2022-06-09 15:14:37 +02:00
Nicolas Vannieuwkerke	81fff7384d	small fix and typo	2022-06-09 15:08:02 +02:00
Nicolas Vannieuwkerke	14d38e43cf	fix test.yml	2022-06-09 14:58:20 +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
nvnieuwk	6d10909e9f	Update tests/modules/ensemblvep/main.nf ... Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>	2022-06-09 11:55:41 +02:00
nvnieuwk	e88a4ff70b	Merge branch 'master' into add-optional-fasta-parameter-to-ensemblvep	2022-06-09 11:54:22 +02:00
Nicolas Vannieuwkerke	e60323b757	typo	2022-06-09 11:53:59 +02:00
Nicolas Vannieuwkerke	7947bc662c	added an extra test without fasta	2022-06-09 11:53:16 +02:00
Nicolas Vannieuwkerke	a3202e41ec	prettier	2022-06-09 11:47:24 +02:00
Nicolas Vannieuwkerke	5ccf6fbcc9	add optional fasta argument to ensemblvep	2022-06-09 11:45:27 +02:00
SusiJo	0204d2374b	Merge remote-tracking branch 'origin/master' into gatk_spark	2022-06-09 09:33:17 +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
Taniguti	89bffe3a5e	Merge branch 'master' into haplocheck	2022-06-08 15:00:06 -03:00
Ramprasad Neethiraj	1d67489056	update test	2022-06-08 16:36:02 +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
Taniguti	d037f0ec97	Merge branch 'master' into haplocheck	2022-06-08 10:47:38 -03:00
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	c005a5e007	formatting	2022-06-08 14:42:58 +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
Lucas Taniguti	b2afb3b2ee	fix: string interpolation and test input access	2022-06-08 09:08:59 -03:00
Matthias De Smet	71e3056813	Merge branch 'master' into update/multiqc	2022-06-08 14:03:26 +02:00
Matthias De Smet	439d2a9e67	update mqc inputs	2022-06-08 13:48:27 +02:00
Lucas Taniguti	abaec30889	tests: add stub	2022-06-08 08:46:22 -03:00
Lucas Taniguti	f26979c44e	tests: add input to test_data.config	2022-06-08 08:10:25 -03:00
Taniguti	d5e077a2e9	Merge branch 'master' into haplocheck	2022-06-08 07:31:28 -03:00
Maxime U. Garcia	7230bf2174	Merge branch 'master' into update_tiddit	2022-06-08 11:16:01 +02:00
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
Ramprasad Neethiraj	16e5e6093c	Merge branch 'master' of https://github.com/nf-core/modules into rhocall	2022-06-07 14:45:09 +02:00
SusiJo	745e47cd33	add versions.yml	2022-06-07 14:38:43 +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
Taniguti	a2e2d50494	Merge branch 'master' into haplocheck	2022-06-07 08:16:22 -03:00
Ramprasad Neethiraj	9d6697bdea	template	2022-06-07 12:14:40 +02:00
Nicolas Vannieuwkerke	771425e7a0	add threads to calibratedragstrmodel	2022-06-07 12:11:18 +02:00
SusiJo	1368956d88	Merge remote-tracking branch 'origin/master' into gatk_spark	2022-06-07 11:00:33 +02:00
James A. Fellows Yates	d292f822e4	Merge branch 'master' into gatk-realigntargetcreator	2022-06-03 21:33:22 +02:00
James A. Fellows Yates	d2b240a17a	Merge branch 'master' into gatk-unifiedgenotyper	2022-06-03 21:24:09 +02:00
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
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
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
James Fellows Yates	a565d9072a	Add GATK UnifiedGenotyper	2022-06-02 21:39:39 +02:00
James Fellows Yates	544b62df45	Star work on GATK UG	2022-06-02 21:11:17 +02:00
James Fellows Yates	9a4f22e8d1	Merge branch 'gatk-realigntargetcreator' of github.com:jfy133/nf-core-modules into gatk-realigntargetcreator	2022-06-02 20:32:03 +02:00
James Fellows Yates	c469a2b35e	Fux tests	2022-06-02 20:32:00 +02:00
James A. Fellows Yates	abc619a3e2	Merge branch 'master' into gatk-realigntargetcreator	2022-06-02 20:24:24 +02:00
SusiJo	1b93cde9ff	Merge branch 'master' into gatk_spark	2022-06-02 16:24:39 +02:00
Nicolas Vannieuwkerke	b4b1f3b81d	add intervals to calibratedragstrmodel	2022-06-02 16:20:12 +02:00
nvnieuwk	e107d61069	Update tests/modules/gatk4/haplotypecaller/test.yml ... Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>	2022-06-02 14:20:15 +02:00
nvnieuwk	e419d306df	Update tests/modules/gatk4/haplotypecaller/test.yml ... Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>	2022-06-02 14:20:10 +02:00
nvnieuwk	2ce1cf3329	Update tests/modules/gatk4/haplotypecaller/test.yml ... Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>	2022-06-02 14:20:04 +02:00
nvnieuwk	a6c4276ad7	Update tests/modules/gatk4/haplotypecaller/test.yml ... Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>	2022-06-02 14:19:57 +02:00
Nicolas Vannieuwkerke	e53d091a6d	added dragstr model to haplotypecaller	2022-06-02 14:08:09 +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
Matthias De Smet	f58771c47f	Merge branch 'master' into update/untar	2022-06-02 13:38:53 +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	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	8470f3cb7e	linting	2022-06-01 09:20:20 +02:00
James A. Fellows Yates	5a94794793	Merge branch 'master' into r-ampir	2022-06-01 09:18:54 +02:00
Nicolas Vannieuwkerke	d4f3df4677	Updated the test	2022-06-01 09:17:05 +02:00