1172 commits

Author	SHA1	Message	Date
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
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
James Fellows Yates	de88adc926	Standardise parameters (no tests yet until realigntarget creator ready)	2022-06-02 20:35:34 +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 Fellows Yates	599b264280	Standaridse parameters	2022-06-02 20:27:16 +02:00
James A. Fellows Yates	b1edcc6e94	Update modules/gatk/realignertargetcreator/main.nf	2022-06-02 20:26:09 +02:00
James A. Fellows Yates	43ef3841d1	remove duplciate path	2022-06-02 20:25:12 +02:00
James A. Fellows Yates	abc619a3e2	Merge branch 'master' into gatk-realigntargetcreator	2022-06-02 20:24:24 +02:00
James Fellows Yates	28101149b6	Merge branch 'gatk-realigntargetcreator' of github.com:jfy133/nf-core-modules into gatk-realigntargetcreator	2022-06-02 20:24:17 +02:00
James Fellows Yates	14c63f9ccc	Changes after review	2022-06-02 20:24:14 +02:00
SusiJo	1b93cde9ff	Merge branch 'master' into gatk_spark	2022-06-02 16:24:39 +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
SusiJo	efc1e1bb71	rm line ... Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>	2022-06-02 16:23:18 +02:00
SusiJo	44daa5d687	update prefix ... Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>	2022-06-02 16:23:09 +02:00
nvnieuwk	897de827ee	Merge branch 'master' into add-intervals-to-calibratedragstrmodel	2022-06-02 16:20:41 +02:00
Nicolas Vannieuwkerke	b4b1f3b81d	add intervals to calibratedragstrmodel	2022-06-02 16:20:12 +02:00
MaxUlysse	b623ff5d27	fix comments	2022-06-02 16:11:45 +02:00
MaxUlysse	bc0f52bcd3	fix cache version	2022-06-02 16:11:11 +02:00
MaxUlysse	046fa39582	update VEP version + cache	2022-06-02 16:09:09 +02:00
Nicolas Vannieuwkerke	e53d091a6d	added dragstr model to haplotypecaller	2022-06-02 14:08:09 +02:00
Matthias De Smet	db0dc81b81	Merge branch 'master' into bump/picard	2022-06-02 13:49:03 +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
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
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	45f3795670	Merge branch 'master' into bump/picard	2022-06-02 11:33:26 +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	114a54c8d5	spaces fix	2022-06-01 09:22:09 +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
Alexander Peltzer	9ac3cf342a	Merge branch 'master' into gatk-realigntargetcreator	2022-05-31 21:12:59 +02:00
James Fellows Yates	7633d7816b	Add GATK(3)/realignertargetcreator	2022-05-31 20:35:54 +02:00
James A. Fellows Yates	615cb0722f	Merge branch 'master' into fix-filtlong	2022-05-31 20:25:16 +02:00
James Fellows Yates	d39ba08e02	Prepare main module code	2022-05-31 20:19:49 +02:00
James Fellows Yates	c1ac3fbb59	Skeleton	2022-05-31 20:13:48 +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	80366924fd	added gatk4/composestrtablefile	2022-05-31 16:08:13 +02:00
James Fellows Yates	089f761f0b	Actually add the changes	2022-05-31 15:49:57 +02:00
Anders Sune Pedersen	5513d095f5	Adding tbi-files to the output from GATK4_MERGEVCFS. #1709	2022-05-31 15:37:26 +02:00
SusiJo	49135415ae	Merge branch 'master' into gatk_spark	2022-05-31 15:36:55 +02:00
SusiJo	810564deca	Merge branch 'master' into gatk_spark	2022-05-31 15:24:58 +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	0b895871d7	Merge branch 'master' into fix-filtlong	2022-05-31 14:49:44 +02:00
SusiJo	1e396d767f	Merge remote-tracking branch 'upstream/master' into gatk_spark	2022-05-31 14:36:14 +02:00
SusiJo	39e34418c9	added metrics as optional output	2022-05-31 14:34:50 +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
James Fellows Yates	7ffe98ac8b	Add gatk/indelrealigner	2022-05-30 21:12:21 +02:00
Sébastien Guizard	a3ae526521	Merge branch 'master' into bamtools/convert/remove_TODO	2022-05-30 17:36:36 +01:00
Sebastien Guizard	d463cd5dd6	👌 IMPROVE: Remove last TODO	2022-05-30 17:26:51 +01:00
jtangrot	5f0d75bb37	Merge branch 'vsearch_usearch_global' of https://github.com/jtangrot/nf-core_modules into vsearch_usearch_global	2022-05-30 13:05:00 +02:00
Jeanette Tångrot	69e00b55d3	Update modules/vsearch/usearchglobal/main.nf ... Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com>	2022-05-30 13:03:45 +02:00
jtangrot	c67c15f243	Make input tuple	2022-05-30 13:01:06 +02:00
Matthias De Smet	63db63757c	bump picard versions	2022-05-30 10:15:40 +02:00
jtangrot	2e16c90fce	Fix whitespace	2022-05-30 09:57:05 +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	fb6c7bca3d	Bump container version for STAR to 2.7.10a	2022-05-27 11:35:04 +01:00
Sateesh Peri	ead3679829	Merge branch 'master' into rp3-add-snippy	2022-05-26 03:04:19 -04:00
Harshil Patel	72a31b76eb	Update main.nf	2022-05-25 19:42:15 +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
SusiJo	b34e5ea6bf	rm unnecessary spark_user	2022-05-25 16:38:48 +02:00
Mahesh Binzer-Panchal	c452f56289	Patch mash screen	2022-05-25 12:29:14 +00:00
Jill V. Hagey, PhD	b1dd1d8a52	Merge branch 'nf-core:master' into gamma-update	2022-05-24 19:28:06 -04:00
Mahesh Binzer-Panchal	3d51956b88	Merge branch 'master' into kat_hist	2022-05-24 23:10:13 +02:00
jvhagey	b8aaea7429	updating paths in test.yml	2022-05-24 16:27:00 -04:00
jvhagey	f1fc7fc38e	adding upzip	2022-05-24 15:15:07 -04:00
Ramprasad Neethiraj	fe90615f57	Merge branch 'rhocall' of github.com:genomic-medicine-sweden/modules into rhocall	2022-05-24 16:17:59 +02:00
Ramprasad Neethiraj	b0dba3ee75	update description	2022-05-24 16:17:15 +02:00
Ramprasad Neethiraj	c91947f8a1	Merge branch 'master' into rhocall	2022-05-24 16:07:55 +02:00
Mahesh Binzer-Panchal	9a5d6a815b	Merge branch 'master' into kat_hist	2022-05-24 15:46:12 +02:00
SusiJo	3077e4d34c	Merge branch 'master' into cnvkit/reference	2022-05-24 15:00:29 +02:00
SusiJo	8208140d21	missing meta.id changed	2022-05-24 14:59:52 +02:00
SusiJo	6b425735b9	Merge remote-tracking branch 'origin/master' into cnvkit/reference	2022-05-24 14:20:55 +02:00
SusiJo	749edce069	add prefix	2022-05-24 14:20:19 +02:00
Mahesh Binzer-Panchal	c8ffecfe86	Merge branch 'master' into kat_hist	2022-05-24 13:57:45 +02:00
Matthias De Smet	c51c047b2e	Merge branch 'master' into update/mosdepth	2022-05-24 13:50:22 +02:00
Matthias De Smet	a2a8e09762	Update modules/mosdepth/main.nf ... Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>	2022-05-24 13:45:52 +02:00