719 commits

Author	SHA1	Message	Date
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	3efa931bf6	view	2022-05-03 14:26:46 +02:00
Ramprasad Neethiraj	829c15c98b	partition	2022-05-03 14:26:34 +02:00
Ramprasad Neethiraj	7cc47f6ba6	importrd	2022-05-03 14:25:20 +02:00
Ramprasad Neethiraj	07e026054a	histogram	2022-05-03 14:24:54 +02:00
Ramprasad Neethiraj	2990dc8357	callcnv module	2022-05-03 14:20:05 +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	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
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
nvnieuwk	8187641280	Update modules/vardictjava/meta.yml ... Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>	2022-05-03 10:16:45 +02:00
nvnieuwk	11c6faf433	Update modules/vardictjava/meta.yml ... Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>	2022-05-03 10:16:36 +02:00
nvnieuwk	01085b3e09	Update modules/vardictjava/meta.yml ... Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>	2022-05-03 10:16:30 +02:00
nvnieuwk	1609dfc96d	Update modules/vardictjava/meta.yml ... Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>	2022-05-03 10:16:20 +02:00
nvnieuwk	3cdbdf50fc	Update modules/vardictjava/meta.yml ... Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>	2022-05-03 10:16:14 +02:00
nvnieuwk	2dff193b54	Update modules/vardictjava/meta.yml ... Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>	2022-05-03 10:15:59 +02:00
nvnieuwk	7c89af359c	Update modules/vardictjava/meta.yml ... Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>	2022-05-03 10:15:51 +02:00
Nicolas Vannieuwkerke	49ba3adbde	Merge branch 'vardict-java' of github.com:nvnieuwk/modules into vardict-java	2022-05-03 10:15:33 +02:00
Nicolas Vannieuwkerke	d33253513f	put the version on top of the file	2022-05-03 10:15:30 +02:00
Lauri Mesilaakso	773e6f8e93	Merge branch 'master' into add_compression_to_bam2fq	2022-05-03 11:13:55 +03:00
nvnieuwk	278d41b6bf	Merge branch 'master' into vardict-java	2022-05-03 09:59:05 +02:00
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
Nicolas Vannieuwkerke	71c5d21374	ran prettier	2022-05-03 08:34:12 +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
Nicolas Vannieuwkerke	d8782d7976	Merge branch 'vardict-java' of github.com:nvnieuwk/modules into vardict-java	2022-05-03 08:20:13 +02:00
Nicolas Vannieuwkerke	b8a59c2b17	Fixed version annotation	2022-05-03 08:20:10 +02:00
Moritz E. Beber	16aa3915e3	feat: add module for slimfastq	2022-05-02 23:16:59 +02:00
Ramprasad Neethiraj	3194729f82	Merge branch 'master' into adding_stub_to_modules	2022-05-02 18:31:55 +02:00
JIANHONG OU	5735f515f8	fix a typo in version export.	2022-05-02 12:25:48 -04:00
Sateesh Peri	c56b371713	Merge branch 'master' into srst2/srst2	2022-05-02 12:13:11 -04:00
Carpanzano	c07ae8c483	fixed lint in ktimporttaxonomy	2022-05-02 17:47:45 +02:00
Simone Carpanzano	3d9c8a6bb1	Merge branch 'master' into firstbranch	2022-05-02 17:43:33 +02:00
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
JIANHONG OU	250d64dfde	fix the typo of motus_downloadb.	2022-05-02 08:52:54 -04:00
JIANHONG OU	b14f30936e	Merge branch 'nf-core:master' into motus_downloaddb	2022-05-02 08:42:09 -04:00
JIANHONG OU	31dd31079d	update teh versions.yml	2022-05-02 08:41:41 -04:00
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
Matthias De Smet	bf416f2307	Merge branch 'master' into vardict-java	2022-05-02 10:43:47 +02:00
Lucpen	6b64f9cb6c	feat added stub to modules	2022-05-02 10:34:14 +02:00
Ramprasad Neethiraj	d2004a2b76	update cnvpytor	2022-05-01 21:14:01 +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
Simone Carpanzano	2efa5a09ab	Update main.nf ... $args line 28	2022-04-29 00:00:13 +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
Robert A. Petit III	4b6ee6fc14	Merge branch 'master' into rp3-add-shigatyper	2022-04-28 09:51:36 -06:00
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
Nicolas Vannieuwkerke	d626a1dcd3	Removed a whitespace in meta.yml...	2022-04-28 15:41:43 +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
Nicolas Vannieuwkerke	6678ad4426	Added a header to the VCF	2022-04-28 14:54:20 +02:00