518 commits

Author	SHA1	Message	Date
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	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
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
Sateesh Peri	c56b371713	Merge branch 'master' into srst2/srst2	2022-05-02 12:13:11 -04:00
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
Jasmin F	235944f797	Merge branch 'master' into antismash_db_output	2022-05-02 17:11:51 +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
Lucpen	dfabf960dc	Merge branch 'master' into adding_stub_to_modules	2022-05-02 14:20:03 +02:00
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
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
Harshil Patel	4df985a065	Merge branch 'master' into tool/bamtools-split	2022-04-29 16:38:59 +01:00
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
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
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