1291 commits

Author	SHA1	Message	Date
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
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
Mahesh Binzer-Panchal	58ea709f7f	Merge branch 'master' into busco	2022-05-05 09:34:14 +02:00
ljmesi	888e122f05	Merge branch 'add_compression_to_bam2fq' of https://github.com/Genomic-Medicine-Linkoping/modules into add_compression_to_bam2fq	2022-05-05 08:32:48 +02:00
ljmesi	be8ce6de2a	Remove variable md5sum from the tests	2022-05-05 08:32:45 +02:00
James A. Fellows Yates	35b5ba673f	Merge branch 'master' into motus_downloaddb	2022-05-04 20:58:08 +02:00
Lauri Mesilaakso	e757966566	Merge branch 'master' into add_compression_to_bam2fq	2022-05-04 18:41:36 +03:00
Carpanzano	38faf040ec	missing change in ext.args config	2022-05-04 16:54:15 +02:00
Nicolas Vannieuwkerke	3c07602443	Added the version.yml	2022-05-04 16:51:09 +02:00
Carpanzano	e7b92a7616	fixing md5sum changes	2022-05-04 16:43:22 +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	42bdc5471e	Changed the pytest location of happy	2022-05-04 15:40:34 +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	3c66138672	Linting issue + removed the contains lines	2022-05-04 14:49:17 +02:00
Nicolas Vannieuwkerke	5889d6c923	Another possible fix for the pytest issues	2022-05-04 14:46:15 +02:00
Nicolas Vannieuwkerke	583ea13800	Another try to fix the pytest issues	2022-05-04 14:22:55 +02:00
Nicolas Vannieuwkerke	17dbd2bb82	Linting issue fixed	2022-05-04 14:18:56 +02:00
Nicolas Vannieuwkerke	c1393bf999	Possible fix for the pytest errors?	2022-05-04 14:14:01 +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
Mahesh Binzer-Panchal	f65abe1e9a	Prettier	2022-05-04 11:54:51 +00:00
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
Mahesh Binzer-Panchal	8df20218bf	Add more tests and capture summaries ... Co-authored-by: Jill V. Hagey, PhD <jvhagey@gmail.com>	2022-05-04 09:22:43 +00:00
Mahesh Binzer-Panchal	3bb0711b06	Merge branch 'master' into busco	2022-05-04 09:15:46 +02:00
Lauri Mesilaakso	530b5ac661	Merge branch 'master' into add_compression_to_bam2fq	2022-05-04 09:53:46 +03:00
Chris Cheshire	79e64cdd1f	Merge branch 'master' into expected_error_fix	2022-05-03 22:21:28 +01:00
Lauri Mesilaakso	12f79c2101	Merge branch 'master' into add_compression_to_bam2fq	2022-05-03 17:03:02 +03:00
ljmesi	a39fa4e003	Fix checksum for one file	2022-05-03 15:47:49 +02:00
Mahesh Binzer-Panchal	636abad8f1	Merge branch 'master' into busco	2022-05-03 15:38:25 +02:00
Nicolas Vannieuwkerke	96d4a31cc1	Moved the BED file to the main tuple	2022-05-03 15:31:05 +02:00
Mahesh Binzer-Panchal	5f4781adaa	Merge branch 'master' into busco	2022-05-03 15:27:10 +02:00
Mahesh Binzer-Panchal	57db28386e	Support batch fasta analysis	2022-05-03 13:26:49 +00:00
ljmesi	034352dbbf	Merge branch 'add_compression_to_bam2fq' of https://github.com/Genomic-Medicine-Linkoping/modules into add_compression_to_bam2fq	2022-05-03 15:18:12 +02:00
ljmesi	5510ea39fe	Test --no-name to solve inconsistent checksums	2022-05-03 15:18:09 +02:00
Ramprasad Neethiraj	26311aba2a	fix minor errors	2022-05-03 15:04:37 +02:00
Ramprasad Neethiraj	be085c0173	Merge branch 'master' of https://github.com/nf-core/modules into feat/update_cnvpytor	2022-05-03 14:55:42 +02:00
Ramprasad Neethiraj	19cfb4e951	update meta files	2022-05-03 14:53:56 +02:00
Ramprasad Neethiraj	46e5752b82	update tests	2022-05-03 14:32:45 +02:00
Lauri Mesilaakso	a65e76e3dd	Merge branch 'master' into add_compression_to_bam2fq	2022-05-03 14:30:54 +03:00
Chris Cheshire	6f35537d40	Merge branch 'master' into expected_error_fix	2022-05-03 12:21:51 +01:00
Chris Cheshire	829183ee84	Merge branch 'master' into rp3-add-shigatyper	2022-05-03 12:16:54 +01:00
Chris Cheshire	6015478b72	Merge branch 'master' into add-slimfastq	2022-05-03 12:11:19 +01:00
Chris Cheshire	d7fb969a74	Merge branch 'master' into rp3-add-shigatyper	2022-05-03 12:10:23 +01:00
Chris Cheshire	40e6bd9dc1	bowtie2|fix tags error	2022-05-03 12:07:04 +01:00
Chris Cheshire	0f1ee7e50d	bowtie2|test fixes	2022-05-03 12:04:51 +01:00
Chris Cheshire	61f68913fe	Merge branch 'master' into expected_error_fix	2022-05-03 11:49:35 +01:00
Chris Cheshire	768073be63	bowtie2|Added support for large indexes	2022-05-03 11:46:19 +01:00
Mahesh Binzer-Panchal	ddbe6e8f40	Merge branch 'master' into busco	2022-05-03 10:48:03 +02:00
Mahesh Binzer-Panchal	9a72548ee1	Update busco module	2022-05-03 08:42:56 +00:00
Lauri Mesilaakso	6367c6a1ad	Merge branch 'master' into add_compression_to_bam2fq	2022-05-03 11:41:25 +03:00
nvnieuwk	f85787b19e	Merge branch 'master' into vardict-java	2022-05-03 10:17:04 +02:00
Lauri Mesilaakso	773e6f8e93	Merge branch 'master' into add_compression_to_bam2fq	2022-05-03 11:13:55 +03:00
ljmesi	59d6e6e1dd	Add updated md5sums	2022-05-03 09:56:50 +02:00
Ramprasad Neethiraj	6f787aea71	Merge branch 'master' into adding_stub_to_modules	2022-05-03 09:43:16 +02:00
Nicolas Vannieuwkerke	9127f92ddd	Merge branch 'vardict-java' of github.com:nvnieuwk/modules into vardict-java	2022-05-03 08:29:50 +02:00
Nicolas Vannieuwkerke	9a10e5beb5	Added the missing inputs in meta.yml + correct notation	2022-05-03 08:29:46 +02:00
Matthias De Smet	1687bfcb85	Merge branch 'master' into add-slimfastq	2022-05-03 08:22:49 +02:00
Matthias De Smet	a67c06af81	Merge branch 'master' into vardict-java	2022-05-03 08:22:19 +02:00
Jill V. Hagey, PhD	23cfb5dd42	Update test.yml	2022-05-02 18:38:48 -04:00
Jill V. Hagey, PhD	db9681029c	Update test.yml	2022-05-02 18:27:01 -04:00
Jill V. Hagey, PhD	7b0d6f96fd	Update test.yml	2022-05-02 18:20:54 -04:00
Jill V. Hagey, PhD	e5d7c80bb5	Update test.yml	2022-05-02 18:13:14 -04:00
Moritz E. Beber	16aa3915e3	feat: add module for slimfastq	2022-05-02 23:16:59 +02:00
Carpanzano	d2e1408b0f	updated content for html file in test yml	2022-05-02 18:44:05 +02:00
carpanz	e8b2445878	updated file location in test yml	2022-05-02 18:43:20 +02:00
Carpanzano	1deb789502	synced withName ext.args with process name	2022-05-02 18:39:45 +02:00
Carpanzano	5136ed29c4	removed include and changed process name due to expected folder name before tokenize	2022-05-02 18:38:59 +02:00
Ramprasad Neethiraj	3194729f82	Merge branch 'master' into adding_stub_to_modules	2022-05-02 18:31:55 +02:00
Jill V. Hagey, PhD	99a8711997	Update tests/modules/srst2/srst2/test.yml ... Co-authored-by: Edmund Miller <edmund.a.miller@gmail.com>	2022-05-02 12:26:56 -04:00
Carpanzano	32b8f3f612	adding contain for html output in test yml	2022-05-02 18:21:26 +02:00
carpanz	6e83196634	updating test yml after removing kronadb from test	2022-05-02 18:20:36 +02:00
Carpanzano	b0a2d36ec1	removing kronadb module from testing ktimporttaxonomy test - NB: temporarily using test db while testdb is added to test-datasets	2022-05-02 18:16:08 +02:00
Sateesh Peri	c56b371713	Merge branch 'master' into srst2/srst2	2022-05-02 12:13:11 -04:00
Simone Carpanzano	3d9c8a6bb1	Merge branch 'master' into firstbranch	2022-05-02 17:43:33 +02:00
Carpanzano	c9ab26ba8e	synced name of report as in test config	2022-05-02 17:41:55 +02:00
Carpanzano	76a0e3ef04	updated config kraken report name	2022-05-02 17:40:50 +02:00
jvhagey	cd45dc1550	linting test.yml	2022-05-02 11:38:39 -04:00
jvhagey	24dc2d2113	added tests	2022-05-02 11:30:19 -04:00
Carpanzano	1188264fa2	finished test yml file	2022-05-02 17:25:58 +02:00
carpanz	028dc3cb87	updated test yml file	2022-05-02 17:24:55 +02:00
Carpanzano	3cebcbfc0a	remove taxonomy not used in place of db	2022-05-02 17:13:58 +02:00
Carpanzano	2e4c200a26	remove new line between includes	2022-05-02 17:13:20 +02:00
Jasmin F	235944f797	Merge branch 'master' into antismash_db_output	2022-05-02 17:11:51 +02:00
Carpanzano	700d6ab3f1	errore TDOWNLOAD	2022-05-02 16:55:18 +02:00
Carpanzano	80f107515e	update nextflow.config withName	2022-05-02 16:22:22 +02:00
Carpanzano	42310cbce2	updated config to reflect names in test workflow	2022-05-02 16:14:38 +02:00
Carpanzano	38d9d81aaf	update code	2022-05-02 16:10:57 +02:00
Lucpen	50cc136a78	Update tests/modules/gatk4/mutect2/main.nf ... fix spelling mistake Co-authored-by: Maxime U. Garcia <max.u.garcia@gmail.com>	2022-05-02 15:14:05 +02:00
JIANHONG OU	b14f30936e	Merge branch 'nf-core:master' into motus_downloaddb	2022-05-02 08:42:09 -04:00
Lucpen	dfabf960dc	Merge branch 'master' into adding_stub_to_modules	2022-05-02 14:20:03 +02:00
JIANHONG OU	3f07761da5	remove the output check for the versions.yml.	2022-05-02 08:19:13 -04:00
Lucpen	da82e06354	fix gatk4_mutect2 test	2022-05-02 14:16:07 +02:00
Lucpen	3a4e415fe2	chores adding dummy files for stubs	2022-05-02 13:30:18 +02:00
James A. Fellows Yates	f1c2f624eb	Update tests/modules/diamond/blastx/main.nf ... Co-authored-by: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se>	2022-05-02 13:17:22 +02:00
Lucpen	de40c1bf54	chore removing file from test	2022-05-02 13:15:01 +02:00
James Fellows Yates	bd3bfe0817	Add warn of default being used	2022-05-02 12:41:24 +02:00
James Fellows Yates	67b074382e	Fix tests	2022-05-02 12:29:00 +02:00
Lucpen	08d5acbeb6	feat added tests for stubs	2022-05-02 11:59:08 +02:00
James Fellows Yates	58e5c6aece	Make variables consistent	2022-05-02 11:55:43 +02:00
James Fellows Yates	6986975bc0	Fix output channels allow BLAST table customisation	2022-05-02 11:39:07 +02:00
Matthias De Smet	bf416f2307	Merge branch 'master' into vardict-java	2022-05-02 10:43:47 +02:00
James Fellows Yates	996385fb0f	Remove MD5sumfor DIAMOND DAA file due to occasioanlly variability	2022-05-02 09:36:34 +02:00
Ramprasad Neethiraj	9a9f3e97de	fix md5sums	2022-05-01 21:51:40 +02:00
James Fellows Yates	44ed38beb8	Merge branch 'diamond-update' of github.com:jfy133/nf-core-modules into diamond-update	2022-04-29 21:06:09 +02:00
James Fellows Yates	39530b5ca7	Bump DIAMOND version to 2.0.15	2022-04-29 21:05:12 +02:00
Carpanzano	41fd2d1557	modifiche	2022-04-29 17:52:12 +02:00
Harshil Patel	4df985a065	Merge branch 'master' into tool/bamtools-split	2022-04-29 16:38:59 +01:00
Carpanzano	6bf0a407f6	modifiche nextflow.config	2022-04-29 15:51:27 +02:00
Simone Carpanzano	d9d0eb393b	Update nextflow.config	2022-04-29 15:39:50 +02:00
Carpanzano	20787514d9	modifiche per il test	2022-04-29 15:11:21 +02:00
James A. Fellows Yates	23c42e9b76	Merge branch 'master' into tool/elprep-merge	2022-04-29 15:11:09 +02:00
Matthias De Smet	7de207f93f	Merge branch 'master' into diamond-update	2022-04-29 15:02:54 +02:00
Matthias De Smet	bdbf629d93	Merge branch 'master' into tool/bamtools-split	2022-04-29 14:33:28 +02:00
Matthias De Smet	edadc9d216	Merge branch 'master' into tool/elprep-merge	2022-04-29 14:32:12 +02:00
Matthias De Smet	3997d28a77	Merge branch 'master' into subwf/bam_qc	2022-04-29 11:39:18 +02:00
James A. Fellows Yates	983d61763d	Merge branch 'master' into diamond-update	2022-04-29 10:28:38 +02:00
James Fellows Yates	7df2fae746	Clean up test data	2022-04-29 10:26:38 +02:00
James Fellows Yates	42564565b9	Update diamond/blastx diamond/blastp to support all possible output formats	2022-04-29 10:26:17 +02:00
Matthias De Smet	b2e4342105	fix args in nextflow.config	2022-04-29 10:21:22 +02:00
Matthias De Smet	bda132191d	fix args in nextflow.config	2022-04-29 10:13:39 +02:00
CMGG ICT Team	0e01d703ea	remove version md5sum from fixmateinformation	2022-04-29 10:12:52 +02:00
Matthias De Smet	e263f267a7	Merge branch 'master' into bump/picard	2022-04-29 09:48:15 +02:00
Matthias De Smet	ec10f98d55	picard CollectWgsMetrics: update to new cli args (#1578) ... * update to new cli args * remove bam index from tuple, not needed by program * bump picard version Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com>	2022-04-29 09:32:32 +02:00
Matthias De Smet	b72ec05d69	drop md5sum from versions.yml	2022-04-29 08:19:42 +02:00
Simone Carpanzano	05e283405c	Update test_data.config	2022-04-29 00:13:01 +02:00
Simone Carpanzano	a6026e6d30	Update test_data.config	2022-04-29 00:08:27 +02:00
Simone Carpanzano	a76be27d9f	Update test_data.config	2022-04-29 00:06:55 +02:00
Simone Carpanzano	f13a0070d0	Update test_data.config	2022-04-29 00:04:49 +02:00
Simone Carpanzano	10a3718ad6	Update test_data.config ... add 'metagenome' in sarscov2	2022-04-29 00:03:54 +02:00
Matthias De Smet	da94b776ef	Merge branch 'master' into subwf/bam_qc	2022-04-28 22:12:48 +02:00
Matthias De Smet	4d913d337d	Merge branch 'master' into tool/bamtools-split	2022-04-28 21:17:46 +02:00
Matthias De Smet	a7ed1477ee	Merge branch 'master' into tool/elprep-merge	2022-04-28 21:14:30 +02:00
Sateesh Peri	f5c4aecde5	Merge branch 'master' into srst2/srst2	2022-04-28 13:49:51 -04:00
Robert A. Petit III	4b6ee6fc14	Merge branch 'master' into rp3-add-shigatyper	2022-04-28 09:51:36 -06:00
Jasmin F	39258e53d7	Update checksum in test.yml	2022-04-28 17:09:40 +02:00
Jasmin F	c740853874	Antismash db output patch 1 (#3) ... * Update main.nf * Update meta.yml * Update test.yml	2022-04-28 16:42:44 +02:00
Nicolas Vannieuwkerke	4b04ca22dd	Variable name change for var2vcf conversion arguments	2022-04-28 16:38:49 +02:00
nvnieuwk	a6397fac8f	Merge branch 'master' into vardict-java	2022-04-28 15:34:46 +02:00
Nicolas Vannieuwkerke	bdff37c3d7	Added the statistical tests and conversion to vcf	2022-04-28 15:33:27 +02:00
Praveen Raj S	b3e9b88e80	csi output in TABIX (#1579) ... * Added: csi output to TABIX * Added: tests for csi * Fix tiddit/sv (#1580) * Fix fasta ref option for TIDDIT_SV * Add md5sum's to tiddit/sv tests Co-authored-by: Daniel Cooke <dcooke@well.ox.ac.uk> * Fix: prettier issues Co-authored-by: Daniel Cooke <daniel.cooke@invitae.com> Co-authored-by: Daniel Cooke <dcooke@well.ox.ac.uk>	2022-04-28 14:41:01 +02:00
nvnieuwk	c9404ed266	Merge branch 'master' into vardict-java	2022-04-28 14:30:19 +02:00
JIANHONG OU	cdefbec669	add kimporttext module (#1560) ... * add kimporttext module * fix the Prettier error. * fix the Prettier error. * fix the test.yml * fix the test.yml * Update modules/krona/ktimporttext/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/krona/ktimporttext/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/krona/ktimporttext/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/krona/ktimporttext/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/krona/ktimporttext/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * update the test files; simplify the main script of krona/ktimporttext. * update the test file url for krona ktimporttext Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>	2022-04-28 08:16:26 -04:00