1393 commits

Author	SHA1	Message	Date
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
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
jasmezz	77b5986463	Create ampir module	2022-05-25 13:27:10 +02:00
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
Thiseas C. Lamnidis	6d04395c3c	Merge branch 'master' into sexdeterrmine	2022-05-24 13:17:37 +02:00
Mahesh Binzer-Panchal	afb5f226e6	Merge branch 'master' into kat_hist	2022-05-24 13:06:31 +02:00
Matthias De Smet	858cbe80c6	add must fail test	2022-05-24 12:43:49 +02:00
Matthias De Smet	7e777c6626	add error is is provided twice	2022-05-24 12:25:31 +02:00
Matthias De Smet	b5850fd471	add stub	2022-05-24 12:16:03 +02:00
Harshil Patel	393f23274d	Merge branch 'master' into cnvkit/reference	2022-05-24 11:14:50 +01:00
Harshil Patel	29a4f112be	Update main.nf	2022-05-24 11:14:32 +01:00
Matthias De Smet	01fb8851c3	mosdept: cram compatiblility	2022-05-24 11:47:58 +02:00
Harshil Patel	ec141dba08	Merge branch 'master' into umitools	2022-05-24 09:23:20 +01:00
SusiJo	5db94ea0ee	changed tag of module	2022-05-24 10:17:41 +02:00
Ramprasad Neethiraj	b4982ff6e3	Merge branch 'master' into rhocall	2022-05-24 09:41:30 +02:00
SusiJo	0f0d555f96	Merge branch 'master' into cnvkit_reference	2022-05-24 08:03:44 +02:00
SusiJo	0708f343de	Merge branch 'master' into cnvkit_bam	2022-05-24 07:49:51 +02:00
SusiJo	50128b0c86	Merge branch 'master' into cnvkit_reference	2022-05-24 07:49:44 +02:00
SusiJo	63c038ad68	Merge branch 'nf-core:master' into cnvkit_bam	2022-05-24 07:37:24 +02:00
SusiJo	b3e2f70651	Merge branch 'master' into cnvkit/antitarget	2022-05-24 07:36:07 +02:00
SusiJo	33a72367c6	Merge branch 'nf-core:master' into cnvkit_reference	2022-05-24 07:30:29 +02:00
Harshil Patel	84f02a08a5	Update umitools/dedup module to make --output-stats optional	2022-05-23 22:31:09 +01:00
Sateesh Peri	da0ead705e	Merge branch 'master' into update/picard	2022-05-23 13:38:18 -04:00
SusiJo	58c5ec2f4e	rm line ... Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>	2022-05-23 18:53:28 +02:00
SusiJo	86b5951c14	rm line ... Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>	2022-05-23 18:48:30 +02:00
SusiJo	24905e26e2	rm line ... Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>	2022-05-23 18:48:13 +02:00
SusiJo	ddb964a4bf	rm line ... Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>	2022-05-23 18:48:04 +02:00
SusiJo	bbee9e3c3b	add new module cnvkit/reference	2022-05-23 18:35:50 +02:00
Thiseas Christos Lamnidis	37c6fb8fed	Merge remote-tracking branch 'upstream/master' into sexdeterrmine	2022-05-23 17:30:21 +02:00
SusiJo	5d5eacee63	Merge branch 'nf-core:master' into cnvkit/antitarget	2022-05-23 16:52:33 +02:00
SusiJo	4f9d672e55	added new module cnvkit/antitarget	2022-05-23 16:52:06 +02:00
FriederikeHanssen	754afa9ff3	Merge branch 'master' into gatk_filter	2022-05-23 15:37:44 +02:00
Ramprasad Neethiraj	9fb327fec7	Merge branch 'master' of https://github.com/nf-core/modules into rhocall	2022-05-23 13:06:00 +02:00
Rike	175ea9b7f9	fix version	2022-05-23 12:15:33 +02:00
SusiJo	fd31f64266	Merge branch 'master' into cnvkit_bam	2022-05-23 11:31:56 +02:00
Mahesh Binzer-Panchal	e06fb752c3	Merge branch 'master' into kat_hist	2022-05-23 08:52:13 +02:00
Rike	5d72500d60	remove variables used for test data generation, add tbi	2022-05-22 13:34:56 +02:00
Matthias De Smet	c390385cf5	revert wgsmetrics'	2022-05-22 06:44:17 +02:00
Matthias De Smet	d6a0238cd1	Merge branch 'master' into update/picard	2022-05-21 08:34:33 +02:00
Matthias De Smet	a5a6973fcf	picard: make reference sequence optional	2022-05-21 08:33:49 +02:00
Ramprasad Neethiraj	635edc0022	fix typo	2022-05-20 17:07:42 +02:00
Ramprasad Neethiraj	2542c9d176	add tests	2022-05-20 16:46:19 +02:00
Mahesh Binzer-Panchal	2926ec0abb	Add mash screen	2022-05-20 13:23:11 +00:00
Ramprasad Neethiraj	c70b169f61	create modules	2022-05-20 13:34:54 +02:00
SusiJo	9096be5464	improve readability	2022-05-20 13:29:49 +02:00
SusiJo	bdf222649d	remove unnecessary if statement	2022-05-20 13:25:57 +02:00
SusiJo	153c900d0e	refine comment ... Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>	2022-05-20 13:08:38 +02:00
SusiJo	2e5aa0dbb4	refine comment ... Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>	2022-05-20 13:08:26 +02:00
SusiJo	3b3921cfa3	refine comment ... Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>	2022-05-20 13:07:57 +02:00
SusiJo	f392c4bed5	removed params section & added description fasta	2022-05-20 13:05:43 +02:00
SusiJo	129270d7bc	adjusted conda env & singularity container	2022-05-20 10:37:46 +02:00
SusiJo	dd2f48810a	Merge branch 'nf-core:master' into cnvkit_bam	2022-05-20 09:14:21 +02:00
SusiJo	5a1297cc7d	added optional pdf/png outputs	2022-05-20 09:12:47 +02:00
SusiJo	064712c4ea	added cram_bam conversion & tumor_only check	2022-05-20 09:11:45 +02:00
Rike	bb3e64647b	Merge remote-tracking branch 'origin/master' into gatk_filter	2022-05-18 15:52:47 +02:00
FriederikeHanssen	44e9cf56fa	Merge branch 'master' into gatk_cnnscore	2022-05-18 15:32:36 +02:00
Rike	e8221cf98e	Merge remote-tracking branch 'origin' into gatk_cnnscore	2022-05-18 14:27:25 +02:00
Rike	10840a0562	Conda not suported	2022-05-18 14:26:21 +02:00
James A. Fellows Yates	965fabdd54	Merge branch 'master' into motus_profile	2022-05-18 11:25:48 +01:00
Rike	5ae757121f	Add indices and meta	2022-05-17 23:38:26 +02:00
Rike	05837a011d	Add comment	2022-05-17 23:06:52 +02:00
Rike	15fba1dd7c	add filter variant tranches	2022-05-17 23:01:24 +02:00
Rike	e0fcbb428d	Add CNNScoreVariants	2022-05-17 19:09:46 +02:00
Jose Espinosa-Carrasco	3614c19206	Merge branch 'master' into biobambam/bammerge	2022-05-17 15:07:37 +02:00
Nicolas Vannieuwkerke	6342f5b099	added bedtools split	2022-05-17 14:24:32 +02:00
Matthias De Smet	f48790a728	replace regex with fixed extensions	2022-05-17 09:54:06 +02:00
Matthias De Smet	94733a85c0	Update modules/biobambam/bammerge/main.nf ... Co-authored-by: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se>	2022-05-17 09:46:19 +02:00
Matthias De Smet	d3ddc2221a	Merge branch 'master' into biobambam/bammerge	2022-05-17 08:26:28 +02:00
Matthias De Smet	6be91ce82d	fix optional output detection	2022-05-17 08:20:47 +02:00
Subazini TK	79c2c529fc	Merge branch 'master' into hmtnote	2022-05-17 08:05:47 +02:00
JIANHONG OU	671bacb6df	Merge branch 'master' into motus_profile	2022-05-16 17:34:49 -04:00
Matthias De Smet	d0db186e84	Merge branch 'master' into biobambam/bammerge	2022-05-16 20:52:48 +02:00
Matthias De Smet	a79b9adeee	address review comments	2022-05-16 20:51:39 +02:00
Subazini TK	00204fa82b	Update main.nf	2022-05-16 15:20:15 +00:00
Subazini TK	a0b46d3f03	Update meta.yml	2022-05-16 15:20:15 +00:00
Subazini TK	eaf81f6835	Update meta.yml	2022-05-16 15:20:15 +00:00
Subazini TK	1c42c97504	Update meta.yml	2022-05-16 15:20:15 +00:00
Subazini TK	8b4c5742c9	Update main.nf	2022-05-16 15:20:15 +00:00
Subazini TK	2a15bc2ac0	Update main.nf	2022-05-16 15:20:15 +00:00
Subazini TK	78dc1af1e6	Update main.nf	2022-05-16 15:20:15 +00:00
sysbiocoder	26f026683b	hmtnote	2022-05-16 15:20:15 +00:00
sysbiocoder	31fc8b560f	hmtnote	2022-05-16 15:20:15 +00:00
Veit Schwämmle	85345e5f61	Merge branch 'master' into maxquant	2022-05-16 16:06:32 +02:00
Praveen Raj S	df2620cfc7	Merge branch 'master' into process_lable_markdup	2022-05-16 15:53:26 +02:00
Matthias De Smet	98f204fd1f	Update modules/biobambam/bammerge/main.nf ... Co-authored-by: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se>	2022-05-16 15:13:54 +02:00
Matthias De Smet	cdbe648400	align	2022-05-16 14:44:32 +02:00
Matthias De Smet	2cca156fed	linting	2022-05-16 14:42:34 +02:00
Matthias De Smet	af69ea749d	add module: biobambam/bammerge	2022-05-16 14:39:58 +02:00
veitveit	12815af53e	ran prettier	2022-05-16 14:30:40 +02:00
Veit Schwämmle	74a1c1400e	Merge branch 'master' into maxquant	2022-05-16 13:26:35 +02:00
Jasmin F	982c9183fa	Merge branch 'master' into antismashlite	2022-05-16 11:42:44 +02:00
Jasmin F	adcfae6cd4	Merge branch 'master' into antismashlite	2022-05-16 10:38:01 +02:00
Rike	ba14355891	revert markduplciatespark changes	2022-05-16 09:54:40 +02:00
FriederikeHanssen	8b4d021189	Merge branch 'master' into gatk_426	2022-05-16 09:50:13 +02:00
Taniguti	ac7fe89a78	Merge branch 'master' into haplocheck	2022-05-13 11:24:10 -03:00
JIANHONG OU	fadb83cf44	Merge branch 'master' into motus_profile	2022-05-13 09:30:20 -04:00
Matthias De Smet	cbc47767f7	add sort option to bowtie2	2022-05-13 15:26:41 +02:00
Nicolas Vannieuwkerke	6427eeeca0	added tmp-dir + alignment correction	2022-05-13 14:35:22 +02:00
Nicolas Vannieuwkerke	1c2a991429	fixed memory warning	2022-05-13 14:25:53 +02:00
Nicolas Vannieuwkerke	d1f824ae66	updated meta.yml	2022-05-13 14:21:48 +02:00
Praveen	e0dccbb5dd	Changed process label to Medium for GATK4/MarkDuplicates	2022-05-13 13:55:14 +02:00
Nicolas Vannieuwkerke	4f6264f7c3	Merge branch 'new-module-gatk4/splitintervals' of github.com:nvnieuwk/modules into new-module-gatk4/splitintervals	2022-05-13 13:48:35 +02:00
Nicolas Vannieuwkerke	9d53577282	linting	2022-05-13 13:48:33 +02:00
nvnieuwk	1d4862ba60	Merge branch 'master' into new-module-gatk4/splitintervals	2022-05-13 13:47:20 +02:00
Nicolas Vannieuwkerke	8a17b6dd0e	added gatk4/splitintervals	2022-05-13 13:46:34 +02:00
Chris Cheshire	9f6a1ae4a4	Merge branch 'master' into bowtie2-test-fix	2022-05-13 12:05:48 +01:00
Taniguti	4728b2bcd2	Merge branch 'master' into haplocheck	2022-05-13 07:49:55 -03:00
Lucas Taniguti	86343cb034	feat: add haplocheck	2022-05-13 07:42:09 -03:00
Mahesh Binzer-Panchal	00826dc2e9	Merge branch 'master' into genomescope2	2022-05-13 11:28:47 +02:00
Nicolas Vannieuwkerke	6fa1c8089a	Added memory allocation to VCFeval	2022-05-13 10:03:20 +02:00
FriederikeHanssen	868150e1af	Merge branch 'master' into gatk_426	2022-05-12 19:33:07 +02:00
Rike	5f7b02189a	reverse again, why did tests pass before	2022-05-12 18:35:51 +02:00
Rike	e3a17b699e	update version	2022-05-12 18:19:33 +02:00
Rike	99880654bf	add output default bam	2022-05-12 18:06:15 +02:00
Rike	3fda3903dc	revert markduplciatespark container	2022-05-12 17:40:42 +02:00
Mahesh Binzer-Panchal	308ab8801d	Merge branch 'master' into kat_hist	2022-05-12 16:52:05 +02:00
Rike	f40cfefc08	leftover fixes from refactoring	2022-05-12 16:47:17 +02:00
Rike	fd7ee6799a	update version also for spark containers	2022-05-12 15:55:11 +02:00
Rike	169b2b96c1	update gatk version	2022-05-12 15:45:21 +02:00
Jasmin F	85b3c2bcf2	Apply suggestions from code review ... Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>	2022-05-12 15:28:19 +02:00
JIANHONG OU	6b960f0e75	fix the typo in motus_profile.	2022-05-12 09:20:32 -04:00
James A. Fellows Yates	3c02e6056c	Merge branch 'master' into antismashlite	2022-05-12 14:53:52 +02:00
Chris Cheshire	90c67794bf	Added extra tests but error with collection	2022-05-12 10:01:33 +01:00
jasmezz	bd4b70439b	Streamlined some output channels, formatted tests main.nf	2022-05-12 10:56:48 +02:00
JIANHONG OU	a2dbef3de3	remove the wrong quotes for motus_profile.	2022-05-11 17:49:12 -04:00
Robert A. Petit III	8b6e1aff38	Merge branch 'master' into rp3-add-snippy	2022-05-11 12:28:27 -06:00
JIANHONG OU	aca4b48842	Merge branch 'motus_profile' of github.com:jianhong/modules into motus_profile	2022-05-11 14:23:25 -04:00
JIANHONG OU	ae81311a78	fix the typo when using getExtension for motus_profile.	2022-05-11 14:23:09 -04:00
Matthias De Smet	dcf9c07fc9	Merge branch 'master' into update/bowtie2-align	2022-05-11 19:08:23 +02:00
Moritz E. Beber	b2dbaa9930	refactor: rename module	2022-05-11 17:33:45 +02:00
Moritz E. Beber	23091aabda	refactor: move files to custom section	2022-05-11 17:33:45 +02:00
Moritz E. Beber	e4551a9ab3	refactor: always output settings	2022-05-11 17:33:45 +02:00
Moritz E. Beber	64ff23f3c1	feat: add module that verifies NCBI settings	2022-05-11 17:33:45 +02:00
Mahesh Binzer-Panchal	0199d0efd2	Merge branch 'master' into kat_hist	2022-05-11 16:56:29 +02:00
Matthias De Smet	c8d3de2ad9	restore samtools cmd to defaults	2022-05-11 16:17:30 +02:00
Jasmin F	853e3ec087	Remove commented code ... Co-authored-by: Moritz E. Beber <midnighter@posteo.net>	2022-05-11 15:56:10 +02:00
Matthias De Smet	bcd7fe55b1	Update modules/bowtie2/align/main.nf ... Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>	2022-05-11 13:59:03 +02:00
Matthias De Smet	9097abf277	Update modules/bowtie2/align/main.nf ... Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>	2022-05-11 13:58:58 +02:00
Matthias De Smet	971a889e2a	Update modules/bowtie2/align/main.nf ... Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>	2022-05-11 13:57:27 +02:00
Matthias De Smet	b456d8fa0a	Update modules/bowtie2/align/main.nf ... Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>	2022-05-11 13:57:19 +02:00
Matthias De Smet	ff4b297827	Update modules/bowtie2/align/main.nf ... Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>	2022-05-11 13:57:11 +02:00
Matthias De Smet	9dd083fa94	Update modules/bowtie2/align/main.nf ... Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>	2022-05-11 13:55:55 +02:00
Matthias De Smet	dcffd93875	Merge branch 'master' into update/bowtie2-align	2022-05-11 13:34:24 +02:00
CMGG ICT Team	3ae8cbfad7	bowtie2: remove code duplication	2022-05-11 13:32:56 +02:00
Moritz E. Beber	0cdf7767a7	refactor: require NCBI user settings always	2022-05-11 13:02:52 +02:00
Moritz E. Beber	d4f13ebfff	refactor: create new settings input	2022-05-11 12:47:54 +02:00
Moritz E. Beber	5d593bdb45	docs: correct license and input description	2022-05-11 12:47:54 +02:00
Mahesh Binzer-Panchal	fd579ebbb3	Merge branch 'master' into kat_hist	2022-05-11 12:43:11 +02:00
Mahesh Binzer-Panchal	00fcdd0cba	Merge branch 'master' into genomescope2	2022-05-11 12:42:39 +02:00
Mahesh Binzer-Panchal	d54cf467f4	Update outputs and test data set	2022-05-11 10:42:17 +00:00
Harshil Patel	7be7f404d5	Merge branch 'master' into refactor-prefetch	2022-05-11 11:28:02 +01:00
jasmezz	5d76f1c7ff	Add fasta/gff input option	2022-05-11 12:06:02 +02:00
Jasmin F	9cce4a00b2	Merge branch 'nf-core:master' into antismashlite	2022-05-11 12:03:30 +02:00
Mahesh Binzer-Panchal	0774704038	Merge branch 'master' into genomescope2	2022-05-11 11:38:36 +02:00
Robert A. Petit III	ef2996e4a5	match names in meta and main	2022-05-10 21:47:57 +00:00
Robert A. Petit III	f15848d477	fix typo	2022-05-10 21:44:40 +00:00
Robert A. Petit III	44e13ae439	add module for snippy	2022-05-10 21:31:43 +00:00
Mahesh Binzer-Panchal	cd32c7f744	Merge branch 'master' into kat_hist	2022-05-10 17:03:00 +02:00
Mahesh Binzer-Panchal	b875cfb744	Merge branch 'master' into kat_hist	2022-05-10 14:36:18 +02:00
Praveen Raj S	237971cd15	Merge branch 'master' into master	2022-05-10 14:35:41 +02:00
Nicolas Vannieuwkerke	fa7c947c35	Adjusted meta	2022-05-10 13:33:37 +02:00
Nicolas Vannieuwkerke	b7134855e4	Small update on the output channels	2022-05-10 12:34:52 +02:00
Moritz E. Beber	1b228835e9	refactor: require settings input always	2022-05-10 12:29:42 +02:00
Nicolas Vannieuwkerke	c18391aa49	Updated meta.yml	2022-05-10 12:26:13 +02:00
nvnieuwk	2eb77bd64e	Update modules/rtgtools/vcfeval/main.nf ... Co-authored-by: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>	2022-05-10 12:22:56 +02:00
nvnieuwk	29f2d3c284	Update modules/rtgtools/vcfeval/main.nf ... Co-authored-by: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>	2022-05-10 12:22:49 +02:00
Nicolas Vannieuwkerke	ef4857ec54	Updated meta.yml	2022-05-10 12:20:01 +02:00
Moritz E. Beber	09bfe3c618	Apply suggestions from code review ... Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>	2022-05-10 12:16:57 +02:00
Moritz E. Beber	b1e134fdd7	docs: describe new file input	2022-05-10 12:16:57 +02:00
Moritz E. Beber	f6936e5270	refactor: accept settings as input	2022-05-10 12:16:57 +02:00
Moritz E. Beber	46a9aabfa3	chore: improve license description	2022-05-10 12:16:57 +02:00
Nicolas Vannieuwkerke	f3d5584ab0	Linting	2022-05-10 12:08:23 +02:00
Nicolas Vannieuwkerke	5db26f9f35	Linting	2022-05-10 12:07:11 +02:00
Nicolas Vannieuwkerke	3a064b0a99	Split the output to different channels	2022-05-10 12:05:42 +02:00
Nicolas Vannieuwkerke	e5d091ad4b	Merge branch 'new-module-rtg/vcfeval' of github.com:nvnieuwk/modules into new-module-rtg/vcfeval	2022-05-10 09:35:44 +02:00
Nicolas Vannieuwkerke	c69d5cc23e	Added evaluation-regions and adjusted the output to now contain all output (and not only the summary)	2022-05-10 09:35:42 +02:00
nvnieuwk	95103fbd79	Merge branch 'master' into new-module-rtg/vcfeval	2022-05-10 09:06:34 +02:00
Praveen Raj S	459a2d1759	Merge branch 'master' into master	2022-05-09 22:16:59 +02:00
Mahesh Binzer-Panchal	f65d896f57	create genomescope2 module	2022-05-09 15:09:15 +00:00
Mahesh Binzer-Panchal	705ad7c3a1	Merge branch 'master' into meryl_unionsum	2022-05-09 16:20:01 +02:00
nvnieuwk	aceb5220cf	Merge branch 'master' into new-module-rtg/vcfeval	2022-05-09 16:18:00 +02:00
Mahesh Binzer-Panchal	83a266ea70	Merge branch 'master' into meryl_unionsum	2022-05-09 16:16:08 +02:00
FriederikeHanssen	adc4ff868c	Merge branch 'master' into samtools_convert	2022-05-09 16:15:24 +02:00
Rike	da79396f06	rename aligned to alignment	2022-05-09 16:07:49 +02:00
Rike	5bd456e5e8	rename file_type to output extension	2022-05-09 16:06:22 +02:00
Rike	1de1c2253e	Combine output after code review	2022-05-09 16:04:58 +02:00
Nicolas Vannieuwkerke	bd7e1414a4	Fixed meta.yml	2022-05-09 15:55:48 +02:00
nvnieuwk	4b8bd9ebf9	Merge branch 'master' into new-module-rtg/vcfeval	2022-05-09 15:51:31 +02:00
Nicolas Vannieuwkerke	1b63d03f8e	adjusted the bed variable name	2022-05-09 15:51:19 +02:00
Nicolas Vannieuwkerke	f6262b4a10	fixed some issues	2022-05-09 15:47:07 +02:00
Rike	24d5e7feed	Code review suggestions	2022-05-09 15:42:55 +02:00
Mahesh Binzer-Panchal	8d86988632	Merge branch 'master' into meryl/histogram	2022-05-09 15:39:32 +02:00
Rike	ef5f145342	Generalize Bam2Cram do either conversion	2022-05-09 15:22:54 +02:00
Mahesh Binzer-Panchal	57fee2b3d6	Add description pattern	2022-05-09 12:56:22 +00:00
Annick Renevey	bf91f9dd9b	update arriba module	2022-05-09 14:55:59 +02:00
Mahesh Binzer-Panchal	6621768550	Update pytest outputs	2022-05-09 12:54:31 +00:00
Mahesh Binzer-Panchal	ce97c87b5d	Merge branch 'master' into meryl_unionsum	2022-05-09 13:51:55 +02:00
Mahesh Binzer-Panchal	7a5d5f5766	Merge branch 'master' into kat_hist	2022-05-09 13:18:18 +02:00
Mahesh Binzer-Panchal	a43bc940d6	Add suggestions from code review	2022-05-09 11:15:14 +00:00
Mahesh Binzer-Panchal	129f57ccd9	Add meryl histogram	2022-05-09 08:50:28 +00:00
Mahesh Binzer-Panchal	ad4f8389cb	Add meryl unionsum	2022-05-09 08:33:21 +00:00
Mahesh Binzer-Panchal	32b0fdc9d9	Merge branch 'master' into meryl_count	2022-05-09 10:05:28 +02:00
Mahesh Binzer-Panchal	4591ea2205	atomize	2022-05-09 07:58:58 +00:00
Matthias De Smet	2b91985aa0	Merge branch 'master' into new-module-rtg/vcfeval	2022-05-09 09:43:48 +02:00
Nicolas Vannieuwkerke	d18af7358a	Moved untarring the genome sdf folder to the test itself	2022-05-09 09:20:42 +02:00
James A. Fellows Yates	8a83ad0518	Merge branch 'master' into motus_profile	2022-05-09 08:16:16 +02:00
nvnieuwk	6fd9246aef	Update modules/rtgtools/vcfeval/main.nf ... Co-authored-by: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>	2022-05-09 08:07:33 +02:00
JIANHONG OU	b2542ee079	remove the mgc in metadata for motus_profile.	2022-05-08 06:21:26 -04:00
Harshil Patel	2676f8eef4	Merge branch 'master' into fix-prefetch	2022-05-06 19:33:44 +01:00
Matthias De Smet	0752b82c9f	Merge branch 'master' into update/snapaligner	2022-05-06 18:57:37 +02:00
Moritz E. Beber	ea41c753c0	fix: remove retry label ... Call gets retried by bash script	2022-05-06 17:28:56 +02:00
Moritz E. Beber	dd1c66783a	refactor: use a template to add retrying	2022-05-06 17:26:41 +02:00
Moritz E. Beber	ed09978222	chore: update build number	2022-05-06 17:26:41 +02:00
Mahesh Binzer-Panchal	67481c6d54	Start Meryl count	2022-05-06 15:04:04 +00:00
Mahesh Binzer-Panchal	1e55ad987f	Merge branch 'master' into kat_hist	2022-05-06 16:35:51 +02:00
Nicolas Vannieuwkerke	eb8688d2b8	Merge branch 'new-module-rtg/vcfeval' of github.com:nvnieuwk/modules into new-module-rtg/vcfeval	2022-05-06 16:21:35 +02:00
Nicolas Vannieuwkerke	e271410017	Removed some whitespaces	2022-05-06 16:21:32 +02:00
nvnieuwk	5153e10840	Merge branch 'master' into new-module-rtg/vcfeval	2022-05-06 16:19:17 +02:00
JIANHONG OU	9b50036e9b	add test_bam and -m parameter for motus_profile	2022-05-06 08:56:42 -04:00
JIANHONG OU	c301a406dd	Merge branch 'nf-core:master' into motus_profile	2022-05-06 08:33:43 -04:00
Nicolas Vannieuwkerke	84b354ab6a	Added the rtgtools/vcfeval module	2022-05-06 14:23:40 +02:00
JIANHONG OU	3499314b96	Update modules/motus/profile/meta.yml ... Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>	2022-05-06 08:19:47 -04:00
JIANHONG OU	4df57b03bd	Update modules/motus/profile/meta.yml ... Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>	2022-05-06 08:11:58 -04:00
JIANHONG OU	6b2f16a0f4	Update modules/motus/profile/meta.yml ... Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>	2022-05-06 08:11:39 -04:00
JIANHONG OU	baeb2bd1c1	Update modules/motus/profile/main.nf ... Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>	2022-05-06 08:11:29 -04:00
JIANHONG OU	4497eb1734	Update modules/motus/profile/main.nf ... Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>	2022-05-06 08:11:22 -04:00
Matthias De Smet	3930ba227b	merge snapaligner modes into one	2022-05-06 14:10:44 +02:00
Mahesh Binzer-Panchal	9fa6b6c1fc	Update meta.yml	2022-05-06 11:56:43 +00:00
Mahesh Binzer-Panchal	a9f23bb477	Merge branch 'master' into busco	2022-05-06 13:49:01 +02:00
Mahesh Binzer-Panchal	35c5828f43	Add --auto-lineage option and remove single_end ... Co-authored-by: Jill V. Hagey, PhD <jvhagey@gmail.com>	2022-05-06 11:48:21 +00:00
Jose Espinosa-Carrasco	035655e35d	Merge branch 'master' into modules/md5sum	2022-05-06 12:34:14 +02:00
Ramprasad Neethiraj	e639b1e455	Merge branch 'master' into feat/update_cnvpytor	2022-05-06 12:03:12 +02:00
Matthias De Smet	bd1b80f36e	fix software definitions	2022-05-06 11:07:05 +02:00
Ramprasad Neethiraj	1ccea5ff4d	remove prefix def in callcnvs	2022-05-06 10:56:58 +02:00
Matthias De Smet	1c7205d683	fixed container definitions	2022-05-06 10:44:51 +02:00
Matthias De Smet	77d825e043	fix copy paste errors	2022-05-06 10:39:13 +02:00
Matthias De Smet	09e729ad41	added sha256sum	2022-05-06 10:28:14 +02:00
Mahesh Binzer-Panchal	d83281eac9	Merge branch 'master' into kat_hist	2022-05-06 10:02:44 +02:00
Mahesh Binzer-Panchal	9194fb845e	Add module kat hist	2022-05-06 07:54:10 +00:00
Matthias De Smet	853b623969	new module: md5sum	2022-05-06 09:20:40 +02:00
Ramprasad Neethiraj	313d76e005	update svdb version	2022-05-06 00:18:16 +02:00
Ramprasad Neethiraj	af73544010	update meta	2022-05-06 00:13:49 +02:00
Ramprasad Neethiraj	db56d80060	Merge branch 'master' of https://github.com/nf-core/modules into feat/update_cnvpytor	2022-05-06 00:10:28 +02:00
Ramprasad Neethiraj	e4e4f8090c	combine multiple pytor	2022-05-05 23:59:12 +02:00
JIANHONG OU	e391c65510	fix the version issue for motus_profile.	2022-05-05 15:35:31 -04:00
JIANHONG OU	b8efa2ae7c	Merge branch 'master' into motus_profile	2022-05-05 13:41:54 -04:00
JIANHONG OU	fb5c5d310a	update motus module.	2022-05-05 13:38:46 -04:00
Sateesh Peri	faf45edc5e	Merge branch 'master' into busco	2022-05-05 12:48:39 -04:00
Ramprasad Neethiraj	db2acba71b	Merge branch 'master' into feat/update_cnvpytor	2022-05-05 17:31:10 +02:00
Ramprasad Neethiraj	c183d7b397	Merge branch 'feat/update_cnvpytor' of github.com:ramprasadn/modules into feat/update_cnvpytor	2022-05-05 17:28:59 +02:00
Ramprasad Neethiraj	ea1f5daf44	polish python script in view	2022-05-05 17:28:49 +02:00
Harshil Patel	1289626cc9	Update modules/busco/main.nf	2022-05-05 16:09:45 +01:00
Mahesh Binzer-Panchal	2542ae1823	Update modules/busco/main.nf ... Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com>	2022-05-05 16:33:32 +02:00
Sateesh Peri	3414d3aba3	Merge branch 'master' into busco	2022-05-05 10:08:55 -04:00
JIANHONG OU	c8f2c44e22	Merge remote-tracking branch 'origin' into motus_profile	2022-05-05 09:41:13 -04:00
JIANHONG OU	a8bc386ea3	Merge branch 'master' into motus_downloaddb	2022-05-05 09:36:25 -04:00
JIANHONG OU	566c11dacc	Merge branch 'master' into motus_downloaddb	2022-05-05 08:28:10 -04:00
Francesco L	97f318eea6	Merge branch 'master' into firstbranch	2022-05-05 14:25:00 +02:00
Carpanzano	a700a9c15e	Merge branch 'firstbranch' of github.com:carpanz/modules into firstbranch	2022-05-05 13:52:45 +02:00
Carpanzano	9083d3bb3d	integrating suggestions from PR comments, including recovery of tests for kronadb and more detailed explanation of input database in yml file	2022-05-05 13:51:41 +02:00
jasmezz	47a95388c2	Remove trailing whitespaces (ECLint check)	2022-05-05 13:17:36 +02:00
jasmezz	24b9c397dd	Apply suggestions from code review + add support for GFF annotations	2022-05-05 13:14:39 +02:00
MaxUlysse	40dd662fd2	update ensemblvep and snpeff modules	2022-05-05 12:57:14 +02:00
James A. Fellows Yates	e60c6f9bfd	Merge branch 'master' into firstbranch	2022-05-05 10:57:27 +02:00
Carpanzano	204dfba2d8	fixing ktupdatetaxonomy/meta.yml as suggested in PR	2022-05-05 10:51:22 +02:00
Mahesh Binzer-Panchal	865ad3447a	Update meta.yml output files	2022-05-05 08:23:54 +00:00
jasmezz	6a7aec8b41	Remove prokka test workflow	2022-05-05 10:22:02 +02:00
Mahesh Binzer-Panchal	58ea709f7f	Merge branch 'master' into busco	2022-05-05 09:34:14 +02:00
James A. Fellows Yates	6393a085c5	Apply suggestions from code review	2022-05-05 08:23:51 +02:00
JIANHONG OU	29ee72c693	update meta.yml and remove the cleanup step.	2022-05-04 15:37:12 -04:00
JIANHONG OU	e9c82a5f48	Update modules/motus/downloaddb/meta.yml ... Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>	2022-05-04 15:29:06 -04:00
James A. Fellows Yates	35b5ba673f	Merge branch 'master' into motus_downloaddb	2022-05-04 20:58:08 +02:00
James A. Fellows Yates	ec5bada3fc	Update modules/motus/downloaddb/meta.yml	2022-05-04 20:55:16 +02:00
Lauri Mesilaakso	e757966566	Merge branch 'master' into add_compression_to_bam2fq	2022-05-04 18:41:36 +03:00
Carpanzano	a6086f549d	recovered process name	2022-05-04 17:28:24 +02:00
Nicolas Vannieuwkerke	3c07602443	Added the version.yml	2022-05-04 16:51:09 +02:00
Carpanzano	8b1711d8a1	recovering old module name	2022-05-04 16:38:10 +02:00
Simone Carpanzano	162f8edf54	Merge branch 'master' into firstbranch	2022-05-04 16:35:25 +02:00
Carpanzano	6b8ca501ed	fixing suggestions from PR	2022-05-04 16:34:52 +02:00
Nicolas Vannieuwkerke	f875aec46b	Split the module into two parts	2022-05-04 15:29:48 +02:00
Mahesh Binzer-Panchal	5986a3efbf	Merge branch 'master' into busco	2022-05-04 15:09:54 +02:00
Nicolas Vannieuwkerke	505ab03803	fixed a description	2022-05-04 14:14:53 +02:00
Nicolas Vannieuwkerke	177a7e49f2	Fixed a linting issue	2022-05-04 14:06:42 +02:00
Nicolas Vannieuwkerke	000b8ee2e0	Merge branch 'new-module-hap.py' of github.com:nvnieuwk/modules into new-module-hap.py	2022-05-04 14:05:23 +02:00
Nicolas Vannieuwkerke	065a5d6a7f	Fixed a linting issue	2022-05-04 14:05:21 +02:00
nvnieuwk	c9808cb97f	Merge branch 'master' into new-module-hap.py	2022-05-04 14:01:02 +02:00
Nicolas Vannieuwkerke	37338ecee3	Finished the module	2022-05-04 14:00:02 +02:00
Ramprasad Neethiraj	6541e151bc	Merge branch 'master' into feat/update_cnvpytor	2022-05-04 13:54:46 +02:00
Mahesh Binzer-Panchal	73a8df9522	Fix no genes found test and update test.yml	2022-05-04 11:52:42 +00:00
Nicolas Vannieuwkerke	c517ce9b4d	Added the module and some simple testing	2022-05-04 13:42:12 +02:00