1303 commits

Author	SHA1	Message	Date
Thiseas C. Lamnidis	fe855a1c23	Apply suggestions from code review ... Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>	2022-06-10 11:03:01 +02:00
Alexander Peltzer	cfcd93f3e7	Update Dockerfile	2022-06-10 10:56:13 +02:00
Alexander Peltzer	61d87bb2bc	Update main.nf	2022-06-10 10:54:06 +02:00
Alexander Peltzer	e499abe572	Update main.nf	2022-06-10 10:53:48 +02:00
Alexander Peltzer	8032833e6e	Update main.nf	2022-06-10 10:53:09 +02:00
Alexander Peltzer	e36b79201d	Update Dockerfile	2022-06-10 10:52:13 +02:00
James A. Fellows Yates	c9db677a45	Merge branch 'master' into r-ampir	2022-06-09 19:28:37 +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
jasmezz	ba53e09b64	Implement suggestions from code review	2022-06-09 15:37:35 +02:00
Rike	6a4732ef3b	similar issues arise with bqsrspark, also use broadinstitute container	2022-06-09 15:29:00 +02:00
Rike	8e8f4c9c51	remove singulairty container	2022-06-09 15:16:11 +02:00
nvnieuwk	873215c8ae	Update modules/gatk4/reblockgvcf/main.nf ... Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>	2022-06-09 15:11:18 +02:00
Rike	89a6a03e38	fix container tag	2022-06-09 15:09:19 +02:00
Nicolas Vannieuwkerke	81fff7384d	small fix and typo	2022-06-09 15:08:02 +02:00
Rike	b9e397ff15	use broadinstitute container	2022-06-09 15:06:46 +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
Rike	ef5b0dd977	gatk4 version update to 4.2.6.1	2022-06-09 14:54:19 +02:00
nvnieuwk	e88a4ff70b	Merge branch 'master' into add-optional-fasta-parameter-to-ensemblvep	2022-06-09 11:54:22 +02:00
Nicolas Vannieuwkerke	5ccf6fbcc9	add optional fasta argument to ensemblvep	2022-06-09 11:45:27 +02:00
SusiJo	cda434611f	fix conda with openjdk 1.8	2022-06-09 10:24:39 +02:00
SusiJo	0204d2374b	Merge remote-tracking branch 'origin/master' into gatk_spark	2022-06-09 09:33:17 +02:00
James A. Fellows Yates	70f7f07a37	Apply suggestions from code review ... Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>	2022-06-09 08:33:37 +02:00
James Fellows Yates	939653a47e	Changes after code review	2022-06-09 08:26:04 +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	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
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
Ramprasad Neethiraj	c079ee2025	fix test	2022-06-08 14:48:16 +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
Ramprasad Neethiraj	1648d2fcba	add index	2022-06-08 14:36:25 +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
Taniguti	d5e077a2e9	Merge branch 'master' into haplocheck	2022-06-08 07:31:28 -03:00
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
Ramprasad Neethiraj	16e5e6093c	Merge branch 'master' of https://github.com/nf-core/modules into rhocall	2022-06-07 14:45:09 +02:00
Ramprasad Neethiraj	17a4e93142	fix versions.yaml	2022-06-07 14:43:35 +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
Nicolas Vannieuwkerke	4c7ef30fb6	changed to label to medium	2022-06-07 12:17:14 +02:00
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	0d087b4890	Update modules/gatk/realignertargetcreator/main.nf	2022-06-03 21:33:54 +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
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	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
SusiJo	e2bb56608c	change prefix output	2022-06-03 13:50:45 +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
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
James A. Fellows Yates	5a94794793	Merge branch 'master' into r-ampir	2022-06-01 09:18:54 +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