926 commits

Author	SHA1	Message	Date
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
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
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
Nicolas Vannieuwkerke	d4f3df4677	Updated the test	2022-06-01 09:17:05 +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
James Fellows Yates	df22cd80df	Fix config for tests	2022-05-31 20:07:52 +02:00
FriederikeHanssen	19037ed8f4	Merge branch 'master' into get_tbi_files_from_gatk4_mergevcfs	2022-05-31 17:42:27 +02:00
Nicolas Vannieuwkerke	1166fb5150	prettier	2022-05-31 16:13:38 +02:00
Nicolas Vannieuwkerke	ec41ea6082	fix test.yml	2022-05-31 16:12:05 +02:00
Nicolas Vannieuwkerke	80366924fd	added gatk4/composestrtablefile	2022-05-31 16:08:13 +02:00
asp8200	98bb45cf4e	Updating test for gatk4/mergevcfs	2022-05-31 13:59:56 +00:00
James A. Fellows Yates	edc9e83a7d	Merge branch 'master' into fix-filtlong	2022-05-31 15:47:39 +02:00
James Fellows Yates	3e20ca7e9a	Don't hardcode forced output names	2022-05-31 15:46:28 +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 Fellows Yates	430def06fa	Switch from md5sum to string due to conda flakiness	2022-05-31 14:45:41 +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
jtangrot	6ae405c5da	prettier	2022-05-30 13:35:12 +02:00
jtangrot	6aac5c2c40	Update test	2022-05-30 13:30:27 +02:00
jtangrot	c67c15f243	Make input tuple	2022-05-30 13:01:06 +02:00
jtangrot	01d86439f5	Add idcutoff as input	2022-05-30 08:50:27 +02:00
jtangrot	589ce2d73a	Add options for output file type	2022-05-30 08:50:27 +02:00
jtangrot	1c99ffd876	Add vserach usearch_global	2022-05-30 08:50:27 +02:00
Harshil Patel	ad578cafcc	Fix tests	2022-05-27 12:14:10 +01:00
Sateesh Peri	ead3679829	Merge branch 'master' into rp3-add-snippy	2022-05-26 03:04:19 -04:00
Harshil Patel	241a1de035	Update main.nf	2022-05-25 19:38:12 +01:00
Matthias De Smet	bc7002b0c9	Merge branch 'master' into update/mosdepth	2022-05-25 19:20:45 +02:00
Matthias De Smet	72ff2732e3	add all remaining outputs to mosdepth	2022-05-25 19:19:39 +02:00
Mahesh Binzer-Panchal	3d532405a5	Merge branch 'master' into mash_screen_patch	2022-05-25 16:51:42 +02:00
Mahesh Binzer-Panchal	c452f56289	Patch mash screen	2022-05-25 12:29:14 +00:00