1776 commits

Author	SHA1	Message	Date
Alexander Peltzer	8dfe8b795f	Merge remote-tracking branch 'refs/remotes/origin/cellranger-7.0.0' into cellranger-7.0.0	2022-06-10 11:23:15 +02:00
Alexander Peltzer	4928dfad34	Trying to fix tests	2022-06-10 11:22:45 +02:00
Alexander Peltzer	570a43ba4c	Fix tests	2022-06-10 11:21:03 +02:00
Thiseas C. Lamnidis	9948e9fe21	Merge branch 'master' into sexdeterrmine	2022-06-10 11:03:18 +02:00
James A. Fellows Yates	c9db677a45	Merge branch 'master' into r-ampir	2022-06-09 19:28:37 +02:00
jasmezz	5841f11edb	Replace MD5 with contains check	2022-06-09 18:15:27 +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
Rike	30262d1fdd	remove variable checksum	2022-06-09 15:44:12 +02:00
Rike	a5583143c4	update checksum	2022-06-09 15:38:28 +02:00
jasmezz	ba53e09b64	Implement suggestions from code review	2022-06-09 15:37:35 +02:00
Rike	95633c6853	update checksum	2022-06-09 15:30:47 +02:00
Nicolas Vannieuwkerke	c50df9ad04	fix test.yml	2022-06-09 15:14:37 +02:00
Nicolas Vannieuwkerke	81fff7384d	small fix and typo	2022-06-09 15:08:02 +02:00
Nicolas Vannieuwkerke	14d38e43cf	fix test.yml	2022-06-09 14:58:20 +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
nvnieuwk	6d10909e9f	Update tests/modules/ensemblvep/main.nf ... Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>	2022-06-09 11:55:41 +02:00
nvnieuwk	e88a4ff70b	Merge branch 'master' into add-optional-fasta-parameter-to-ensemblvep	2022-06-09 11:54:22 +02:00
Nicolas Vannieuwkerke	e60323b757	typo	2022-06-09 11:53:59 +02:00
Nicolas Vannieuwkerke	7947bc662c	added an extra test without fasta	2022-06-09 11:53:16 +02:00
Nicolas Vannieuwkerke	a3202e41ec	prettier	2022-06-09 11:47:24 +02:00
Nicolas Vannieuwkerke	5ccf6fbcc9	add optional fasta argument to ensemblvep	2022-06-09 11:45:27 +02:00
SusiJo	0204d2374b	Merge remote-tracking branch 'origin/master' into gatk_spark	2022-06-09 09:33:17 +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	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
jvhagey	bb999395aa	fixed pytest_modules.yml	2022-05-24 19:19:38 -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	96260ced83	Add test data to config	2022-05-23 17:15:57 +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
Rike	520dd06ca3	add new testdata	2022-05-22 13:25:39 +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