1249 commits

Author	SHA1	Message	Date
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	1d67489056	update test	2022-06-08 16:36:02 +02:00
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
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	c005a5e007	formatting	2022-06-08 14:42:58 +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	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
Lucas Taniguti	f26979c44e	tests: add input to test_data.config	2022-06-08 08:10:25 -03:00
Taniguti	d5e077a2e9	Merge branch 'master' into haplocheck	2022-06-08 07:31:28 -03:00
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
Ramprasad Neethiraj	16e5e6093c	Merge branch 'master' of https://github.com/nf-core/modules into rhocall	2022-06-07 14:45:09 +02:00
SusiJo	745e47cd33	add versions.yml	2022-06-07 14:38:43 +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
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	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
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
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
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
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 A. Fellows Yates	abc619a3e2	Merge branch 'master' into gatk-realigntargetcreator	2022-06-02 20:24:24 +02:00
SusiJo	1b93cde9ff	Merge branch 'master' into gatk_spark	2022-06-02 16:24:39 +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
James A. Fellows Yates	5a94794793	Merge branch 'master' into r-ampir	2022-06-01 09:18:54 +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
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	c1ac3fbb59	Skeleton	2022-05-31 20:13:48 +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
SusiJo	84f584875e	change string array	2022-05-31 15:50:31 +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
SusiJo	58389e550d	test json array	2022-05-31 15:41:50 +02:00
SusiJo	49135415ae	Merge branch 'master' into gatk_spark	2022-05-31 15:36:55 +02:00
SusiJo	941760f75d	ran prettier	2022-05-31 15:36:02 +02:00
SusiJo	35e296cd7d	added brackets	2022-05-31 15:35:34 +02:00
SusiJo	37b543e3e7	changed to tab	2022-05-31 15:29:27 +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
SusiJo	9ef09e6add	adjusted newlines	2022-05-31 14:54:39 +02:00
SusiJo	205576279f	ran prettier again	2022-05-31 14:50:55 +02:00
James Fellows Yates	430def06fa	Switch from md5sum to string due to conda flakiness	2022-05-31 14:45:41 +02:00
SusiJo	d484aa1906	adjusted tabs	2022-05-31 14:45:23 +02:00
SusiJo	e083bfafa0	ran prettier	2022-05-31 14:38:45 +02:00
SusiJo	1e396d767f	Merge remote-tracking branch 'upstream/master' into gatk_spark	2022-05-31 14:36:14 +02:00
SusiJo	ea526051a4	new test.yml	2022-05-31 14:35:42 +02:00
SusiJo	3117b2973c	added test for metrics	2022-05-31 14:35:29 +02:00
SusiJo	e0e8273f74	adjusted input to use queryname sorted bams	2022-05-31 14:35:18 +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
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
SusiJo	1400f2e683	fixed tests - mixed chr21 + chr22	2022-05-25 16:38:30 +02:00
SusiJo	dd6d838cd7	override userEmulation	2022-05-25 16:37:44 +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
jvhagey	127665d27b	fixed test.yml	2022-05-24 19:27:09 -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	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
Matthias De Smet	8381a5e5dd	add window test	2022-05-24 14:43:40 +02:00
Matthias De Smet	5bc2d419a9	fix fail test	2022-05-24 13:23:00 +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	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
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	1451d62be4	rm md5sums for empty files	2022-05-24 07:38:53 +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	a3e70777ad	Fix Conda tests	2022-05-23 22:39:12 +01:00
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	8fec7ae321	added new testdata path	2022-05-23 19:01:46 +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
Thiseas Christos Lamnidis	9011fc7212	Corrected test-datasets input	2022-05-23 17:08:40 +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
Thiseas Christos Lamnidis	070dee0f5b	Use newly added test bam	2022-05-23 15:22:22 +02:00
Rike	e34dcdd8bc	add brackets to contains	2022-05-23 13:19:42 +02:00
Rike	dc6ad1bff6	add brackets to contains	2022-05-23 13:07:08 +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	093e3aafdd	contains	2022-05-23 13:04:49 +02:00
Ramprasad Neethiraj	06a3bff201	fix lint error	2022-05-23 12:59:48 +02:00
Rike	a8de9fd085	test path update	2022-05-23 12:53:36 +02:00
Rike	3af61cfbbc	fix input cardinality for index	2022-05-23 12:26:12 +02:00
Rike	a8dac59c50	md5sum not consistent	2022-05-23 12:10:50 +02:00
Rike	2f36a44f61	nf-core create-test-yml	2022-05-23 12:00:31 +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
Mahesh Binzer-Panchal	d7c1fe1477	Update tests/modules/kat/hist/test.yml ... Co-authored-by: Sateesh Peri <105730406+sateeshblue@users.noreply.github.com>	2022-05-23 08:51:49 +02:00
Mahesh Binzer-Panchal	b40b147004	Update tests/modules/kat/hist/test.yml ... Co-authored-by: Sateesh Peri <105730406+sateeshblue@users.noreply.github.com>	2022-05-23 08:51:29 +02:00
Rike	cd60b4c6eb	add in testdata paths	2022-05-22 13:35:35 +02:00
Matthias De Smet	e13fbf423e	fix tests (again)	2022-05-22 06:54:09 +02:00
Matthias De Smet	cbceee9621	fix tests	2022-05-22 06:51:27 +02:00
Matthias De Smet	3a2de0cf6f	update test for wgsmetrics	2022-05-22 06:49:31 +02:00
Matthias De Smet	4da143ce62	add tests	2022-05-22 06:44:17 +02:00
Ramprasad Neethiraj	995bf88327	add stub	2022-05-20 17:10:09 +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	00077c36c8	removed unnecessary fasta for tumor_only_bam	2022-05-20 13:06:16 +02:00
SusiJo	dd2f48810a	Merge branch 'nf-core:master' into cnvkit_bam	2022-05-20 09:14:21 +02:00
SusiJo	3d57caa683	added test & corrected cram input	2022-05-20 09:13:27 +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
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	15fba1dd7c	add filter variant tranches	2022-05-17 23:01:24 +02:00
Rike	afa0f2a995	update test	2022-05-17 22:53:41 +02:00
Rike	265fd882ca	update test	2022-05-17 19:44:48 +02:00
Rike	5f63904a50	update test	2022-05-17 19:37:18 +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	c5627e0274	fix config	2022-05-17 09:09:19 +02:00
Matthias De Smet	743e95c61b	fix config	2022-05-17 09:01:02 +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	252fcb17c4	Update main.nf	2022-05-16 15:20:15 +00:00
Subazini TK	cb21fa0c96	Update main.nf	2022-05-16 15:20:15 +00:00
Subazini TK	cbae48d06d	Update nextflow.config	2022-05-16 15:20:15 +00:00
Subazini TK	541f403963	Update main.nf	2022-05-16 15:20:15 +00:00
Subazini TK	69243db3d7	Update test.yml	2022-05-16 15:20:15 +00:00
Subazini TK	c8c6fdd2e3	Update main.nf	2022-05-16 15:20:15 +00:00
Subazini TK	fb66e8ba97	Update test.yml	2022-05-16 15:20:15 +00:00
Subazini TK	f0713f4723	Update test.yml	2022-05-16 15:20:15 +00:00
Subazini TK	060d33f2c3	Update test.yml	2022-05-16 15:20:15 +00:00
Subazini TK	df8f1eae69	Update test.yml	2022-05-16 15:20:15 +00:00
sysbiocoder	31fc8b560f	hmtnote	2022-05-16 15:20:15 +00:00
Matthias De Smet	af69ea749d	add module: biobambam/bammerge	2022-05-16 14:39:58 +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	eb841d4ea0	revert markduplciatespark changes	2022-05-16 10:33:01 +02:00
FriederikeHanssen	8b4d021189	Merge branch 'master' into gatk_426	2022-05-16 09:50:13 +02:00
Matthias De Smet	5a2e303522	add PE sorted test	2022-05-13 19:16:50 +02:00
Taniguti	ac7fe89a78	Merge branch 'master' into haplocheck	2022-05-13 11:24:10 -03:00
Matthias De Smet	04f82d4d34	fix test name	2022-05-13 15:32:14 +02:00
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	a72f06dfe8	removed versions checksum	2022-05-13 14:27:59 +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	ea55129ba3	Removed version file checksums	2022-05-13 12:20:41 +01:00
Chris Cheshire	9f6a1ae4a4	Merge branch 'master' into bowtie2-test-fix	2022-05-13 12:05:48 +01:00
Chris Cheshire	d816f2bc5d	Reactivated all tests	2022-05-13 12:01:16 +01:00
Taniguti	4728b2bcd2	Merge branch 'master' into haplocheck	2022-05-13 07:49:55 -03:00
Lucas Taniguti	c1ed4e21be	tests: add haplocheck tests	2022-05-13 07:42:34 -03:00
Mahesh Binzer-Panchal	00826dc2e9	Merge branch 'master' into genomescope2	2022-05-13 11:28:47 +02:00
Mahesh Binzer-Panchal	5df0bcf1be	Update tests/modules/genomescope2/test.yml ... Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>	2022-05-13 11:27:42 +02:00
James A. Fellows Yates	2eebab4f35	Update tests/modules/motus/profile/test.yml	2022-05-12 20:55:54 +01:00
James A. Fellows Yates	8dd711aba2	Update tests/modules/motus/profile/main.nf	2022-05-12 20:08:37 +01:00
FriederikeHanssen	868150e1af	Merge branch 'master' into gatk_426	2022-05-12 19:33:07 +02:00
Rike	99880654bf	add output default bam	2022-05-12 18:06:15 +02:00
Rike	8792d102ee	fix test input	2022-05-12 17:37:06 +02:00
Rike	a694267b4b	fix empty index input	2022-05-12 17:01:03 +02:00
Mahesh Binzer-Panchal	308ab8801d	Merge branch 'master' into kat_hist	2022-05-12 16:52:05 +02:00
Rike	b3bd55da76	getpileupsummaries requires intervals files	2022-05-12 16:51:17 +02:00
Rike	15fbf21b28	double tmpdir args removed, porb leftover after massive refactor where we decided to make it mandatory everywhere	2022-05-12 16:16:53 +02:00
Rike	fef5434c4c	Update md5sums	2022-05-12 16:07:12 +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
James A. Fellows Yates	3c02e6056c	Merge branch 'master' into antismashlite	2022-05-12 14:53:52 +02:00
jasmezz	d2ef476321	Fix Prettier linting error	2022-05-12 12:19:50 +02:00
jasmezz	37cc6f250b	Fixed test.yml	2022-05-12 12:14:19 +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
Robert A. Petit III	8b6e1aff38	Merge branch 'master' into rp3-add-snippy	2022-05-11 12:28:27 -06:00
Robert A. Petit III	7ced6e20de	make prettier	2022-05-11 18:00:36 +00:00
Matthias De Smet	dcf9c07fc9	Merge branch 'master' into update/bowtie2-align	2022-05-11 19:08:23 +02:00
Moritz E. Beber	98d8a741ec	tests: add missing paths to config	2022-05-11 18:17:27 +02:00
Moritz E. Beber	888620063b	tests: delete settings for conda	2022-05-11 17:44:49 +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	a83dd33a7e	tests: use remove settings file	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
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	94e8c3a882	Update tests/modules/bowtie2/align/test.yml ... Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>	2022-05-11 13:56:03 +02:00
Matthias De Smet	0d00452eca	Update tests/modules/bowtie2/align/test.yml ... Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>	2022-05-11 13:55:45 +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	eae7161a32	tests: add settings input or not and test all branches	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	2b746abfbe	Fix Prettier linting issue	2022-05-11 12:09:52 +02:00
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	56e94f625e	remove empty file md5	2022-05-10 21:47:11 +00:00
Robert A. Petit III	44e13ae439	add module for snippy	2022-05-10 21:31:43 +00:00
Mahesh Binzer-Panchal	7a16ece747	Change md5sum to contains	2022-05-10 15:13:25 +00:00
Mahesh Binzer-Panchal	cd32c7f744	Merge branch 'master' into kat_hist	2022-05-10 17:03:00 +02:00
Mahesh Binzer-Panchal	9b4923dcd5	Change test files	2022-05-10 15:02:37 +00:00
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	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
Moritz E. Beber	145e2f80e9	tests: run prefetch with and without given settings	2022-05-10 12:16:57 +02:00
Nicolas Vannieuwkerke	3a064b0a99	Split the output to different channels	2022-05-10 12:05:42 +02:00
Nicolas Vannieuwkerke	6008619603	test issue fix?	2022-05-10 10:20:54 +02:00
Nicolas Vannieuwkerke	96c3f895b9	test issue fix?	2022-05-10 10:19:13 +02:00
Nicolas Vannieuwkerke	42fbf80c72	Fixed a test issue with wrong md5sum	2022-05-10 09:57:49 +02:00
Nicolas Vannieuwkerke	f0e8f6ce4d	Linting	2022-05-10 09:36:54 +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
nvnieuwk	4b8bd9ebf9	Merge branch 'master' into new-module-rtg/vcfeval	2022-05-09 15:51:31 +02:00
Mahesh Binzer-Panchal	da93beaf60	Update pytests	2022-05-09 13:50:49 +00:00
Nicolas Vannieuwkerke	f6262b4a10	fixed some issues	2022-05-09 15:47:07 +02:00
Mahesh Binzer-Panchal	8d86988632	Merge branch 'master' into meryl/histogram	2022-05-09 15:39:32 +02:00
nvnieuwk	d6dd4c2e2d	Update tests/modules/rtgtools/vcfeval/test.yml ... Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>	2022-05-09 15:35:16 +02:00
Rike	ef5f145342	Generalize Bam2Cram do either conversion	2022-05-09 15:22:54 +02:00
Annick Renevey	ac3034696b	update md5sum	2022-05-09 15:19:16 +02:00