583 commits

Author	SHA1	Message	Date
Lauri Mesilaakso	773e6f8e93	Merge branch 'master' into add_compression_to_bam2fq	2022-05-03 11:13:55 +03:00
ljmesi	5503903457	Add compression for output fastq file	2022-05-03 09:46:04 +02:00
Ramprasad Neethiraj	6f787aea71	Merge branch 'master' into adding_stub_to_modules	2022-05-03 09:43:16 +02:00
Lauri Mesilaakso	77054795fb	Merge branch 'master' into add_handling_of_alternative_fn_suffix_for_metaphlan3	2022-05-03 09:38:51 +03:00
Ramprasad Neethiraj	3194729f82	Merge branch 'master' into adding_stub_to_modules	2022-05-02 18:31:55 +02:00
Sateesh Peri	c56b371713	Merge branch 'master' into srst2/srst2	2022-05-02 12:13:11 -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
Jasmin F	8db0b754c0	Fix commented-out command	2022-05-02 16:56:39 +02:00
jasmezz	6a9f2077cf	Fix unbound variable crash	2022-05-02 16:41:59 +02:00
Lucpen	62c6123ec4	fix gatk4_mutect2 test by changing main.nf	2022-05-02 15:11:57 +02:00
jasmezz	0fc352188b	Fix conda antismash path	2022-05-02 14:40:35 +02:00
Jasmin F	5cd517e759	Apply suggestions from code review ... Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>	2022-05-02 14:31:40 +02:00
Lucpen	dfabf960dc	Merge branch 'master' into adding_stub_to_modules	2022-05-02 14:20:03 +02:00
ljmesi	ed4dd1a928	Add additional handling of fq.gz file name suffix	2022-05-02 14:16:12 +02:00
Lucpen	f231291e77	fix gatk4_reversam test	2022-05-02 12:58:12 +02:00
James A. Fellows Yates	575258332a	Merge branch 'master' into diamond-update	2022-05-02 12:41:37 +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
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
Praveen	0511e7fbbf	Changed BAI as optional output to handle large genome	2022-05-02 11:35:15 +02:00
Lucpen	8a5bcbc325	fix the stub of gatk4_revertsam	2022-05-02 11:06:08 +02:00
Lucpen	6b64f9cb6c	feat added stub to modules	2022-05-02 10:34:14 +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	9d0f03d96a	Update modules/elprep/merge/main.nf ... Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>	2022-04-29 15:07:09 +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	771d5a19f1	fix reference arg	2022-04-29 11:12:24 +02:00
Matthias De Smet	20ebb89ff9	update to long args	2022-04-29 10:52:40 +02:00
James A. Fellows Yates	983d61763d	Merge branch 'master' into diamond-update	2022-04-29 10:28:38 +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	e263f267a7	Merge branch 'master' into bump/picard	2022-04-29 09:48:15 +02:00
Lauri Mesilaakso	1a5a9e7b40	Fix typo (#1586)	2022-04-29 09:37:23 +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	00467ac64a	update command line syntax for all tools	2022-04-29 07:57:11 +02:00
Matthias De Smet	6ca6de91f8	bump picard version across the board	2022-04-29 07:47:24 +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
Jill V. Hagey, PhD	218769d7df	Update modules/srst2/srst2/main.nf ... Co-authored-by: Edmund Miller <edmund.a.miller@gmail.com>	2022-04-28 14:41:37 -04:00
Jill V. Hagey, PhD	842ae3982b	Update meta.yml	2022-04-28 14:39:02 -04:00
Jill V. Hagey, PhD	9e7e10305b	Update modules/srst2/srst2/meta.yml ... Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com>	2022-04-28 14:02:28 -04:00
Sateesh Peri	f5c4aecde5	Merge branch 'master' into srst2/srst2	2022-04-28 13:49:51 -04:00
Jill V. Hagey, PhD	e29a69077d	add doi	2022-04-28 12:30:04 -04:00
Jill V. Hagey, PhD	5be6afd6b1	changed container	2022-04-28 12:29:39 -04:00
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