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Author	SHA1	Message	Date
Nicolas Vannieuwkerke	f3c0107fa2	added optional to intervals	2022-06-02 16:24:03 +02:00
Nicolas Vannieuwkerke	b4b1f3b81d	add intervals to calibratedragstrmodel	2022-06-02 16:20:12 +02:00
nvnieuwk	59ce1ec348	Merge pull request #1725 from nvnieuwk/add-dragstrmodel-to-haplotypecaller ... add dragstr model to haplotypecaller	2022-06-02 14:31:53 +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	5447395975	Merge pull request #1724 from nvnieuwk/new-module-gatk4/CalibrateDragstrModel ... new module gatk4/calibratedragstrmodel	2022-06-02 13:49:44 +02:00
nvnieuwk	a339f9818a	Merge branch 'master' into new-module-gatk4/CalibrateDragstrModel	2022-06-02 13:42:56 +02:00
Matthias De Smet	22885ce687	Merge pull request #1723 from matthdsm/update/untar ... fix untar output dir	2022-06-02 13:42:46 +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
SusiJo	1c33eeb348	Merge pull request #1719 from SusiJo/cnvkit_bam ... Adjusted CNVKIT/BATCH for germline mode	2022-06-02 13:36:39 +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	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	3294def3fd	Merge pull request #1722 from SusiJo/deeptools_samtools ... Adjust deeptools/bamcoverage with new mulled container	2022-06-02 10:50:05 +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
nvnieuwk	95e8afe627	Merge pull request #1714 from nvnieuwk/new-module-gatk4/ComposeSTRTableFile ... added gatk4/composestrtablefile	2022-06-01 09:33:08 +02:00
Nicolas Vannieuwkerke	114a54c8d5	spaces fix	2022-06-01 09:22:09 +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	5b74a179c3	Update modules/gatk4/composestrtablefile/main.nf ... Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>	2022-06-01 09:14:08 +02:00
nvnieuwk	e4f51d6f59	Merge branch 'master' into new-module-gatk4/ComposeSTRTableFile	2022-06-01 08:59:19 +02:00
James A. Fellows Yates	33af85697b	Merge pull request #1713 from jfy133/fix-filtlong ... Fix filtlong to remove hardcoded output names	2022-05-31 20:50:21 +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	fba7edb652	Merge pull request #1716 from asp8200/get_tbi_files_from_gatk4_mergevcfs ... Get tbi-files from gatk4 mergevcfs	2022-05-31 17:55:06 +02:00
FriederikeHanssen	19037ed8f4	Merge branch 'master' into get_tbi_files_from_gatk4_mergevcfs	2022-05-31 17:42:27 +02:00
asp8200	4199a05aeb	Removing redundant empty line	2022-05-31 15:34:34 +00:00
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 Fellows Yates	089f761f0b	Actually add the changes	2022-05-31 15:49:57 +02:00
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
Anders Sune Pedersen	5513d095f5	Adding tbi-files to the output from GATK4_MERGEVCFS. #1709	2022-05-31 15:37:26 +02:00
nvnieuwk	22a90dbd0f	Merge pull request #1711 from nvnieuwk/add-tbi-to-bcftools-concat ... Added optional input of index files to bcftools/concat	2022-05-31 15:33:10 +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 A. Fellows Yates	94dd8f63df	Merge pull request #1710 from jfy133/fix-filtlong ... Fix filtlong - makes running without shortreads work correctly, and also ensures all tests produce …	2022-05-31 14:54:54 +02:00