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Author	SHA1	Message	Date
Taniguti	d037f0ec97	Merge branch 'master' into haplocheck	2022-06-08 10:47:38 -03:00
Ramprasad Neethiraj	912bc1caf2	Merge pull request #1737 from genomic-medicine-sweden/update_roh ... Update bcftools/roh	2022-06-08 15:10:45 +02:00
Lucas Taniguti	f5615c3db6	fix: stub output name	2022-06-08 10:10:24 -03:00
Ramprasad Neethiraj	3cabdfac20	Merge branch 'master' into update_roh	2022-06-08 15:04:34 +02:00
Matthias De Smet	da4dc255f8	Merge pull request #1735 from matthdsm/update/multiqc ... multiqc: possible fix for name collisions	2022-06-08 15:01:52 +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	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
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	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
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	c03b8780ec	Merge pull request #1730 from FriederikeHanssen/update_tiddit ... Update TIDDIT to 3.0.0	2022-06-08 12:23:06 +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
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
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
Taniguti	a2e2d50494	Merge branch 'master' into haplocheck	2022-06-07 08:16:22 -03:00
nvnieuwk	f147b32fbf	Merge pull request #1733 from nvnieuwk/add-threads-to-calibratedragstrmodel ... add threads to calibratedragstrmodel	2022-06-07 12:22:53 +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	af890b1417	Merge pull request #1729 from jfy133/gatk-unifiedgenotyper ... Add gatk/unifiedgenotyper	2022-06-03 21:31:31 +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	b534b49b49	Merge pull request #1643 from rpetit3/rp3-add-snippy ... add module for snippy	2022-06-03 13:20:57 -06:00
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	24403ce45d	Merge pull request #1707 from matthdsm/bump/picard ... bump picard versions	2022-06-03 06:39:19 +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
nvnieuwk	fcc186d717	Merge pull request #1728 from nvnieuwk/add-intervals-to-calibratedragstrmodel ... add intervals to gatk4/calibratedragstrmodel	2022-06-02 16:28:25 +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