423 commits

Author	SHA1	Message	Date
Anders Goncalves da Silva	ef1e1b2539	Fix indentation ... Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>	2021-02-15 19:51:45 -08:00
Anders Goncalves da Silva	f841483a70	Fix URL for containers	2021-02-15 13:23:35 -08:00
Anders Goncalves da Silva	e8d1171b5d	Make gff a param and not an optional input	2021-02-15 11:50:52 -08:00
Anders Goncalves da Silva	9e3c4e598c	Add meta to ivar variants	2021-02-15 09:29:10 -08:00
Anders Goncalves da Silva	2fe3210f88	Add ivar variants	2021-02-15 09:27:59 -08:00
Harshil Patel	4af9417b6d	Update software/ivar/trim/main.nf	2021-02-13 08:20:06 +00:00
Harshil Patel	a5686ed14e	Update software/ivar/trim/main.nf	2021-02-13 08:19:55 +00:00
Harshil Patel	25f3d46f68	Update software/ivar/trim/meta.yml	2021-02-13 08:17:03 +00:00
Anders Goncalves da Silva	bbdca4fa76	Fix output files	2021-02-12 16:14:46 -08:00
Anders Goncalves da Silva	7c9766962d	Add ivar trim meta.yml	2021-02-12 16:02:48 -08:00
Anders Goncalves da Silva	6dca7799e6	Add ivar trim	2021-02-12 16:02:10 -08:00
Harshil Patel	63a20e7b5c	Merge pull request #168 from JoseEspinosa/bcftools_merge ... Add bcftools merge module	2021-02-12 23:20:30 +00:00
Harshil Patel	c0d128fd39	Update software/bcftools/merge/main.nf	2021-02-12 23:16:52 +00:00
Anders Goncalves da Silva	9268851cde	Remove samtools option ... Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>	2021-02-12 15:09:50 -08:00
Anders Goncalves da Silva	1f66954180	Relabel input parameter ... Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>	2021-02-12 15:09:35 -08:00
JoseEspinosa	5313698705	Add bcftools merge module	2021-02-13 00:08:57 +01:00
Harshil Patel	0580fd8ded	Update software/ivar/consensus/main.nf	2021-02-12 23:02:04 +00:00
Harshil Patel	9e4539473e	Update software/ivar/consensus/main.nf	2021-02-12 23:01:53 +00:00
Harshil Patel	bc5e073cdb	Update software/ivar/consensus/main.nf	2021-02-12 22:57:06 +00:00
Anders Goncalves da Silva	cb19c7b056	Fix trailing whitespace	2021-02-12 14:46:13 -08:00
Anders Goncalves da Silva	b08bf1ea5c	Remove ref to conda build and additional params	2021-02-12 14:43:50 -08:00
Anders Goncalves da Silva	24b212318b	Merge branch 'master' into ivar-consensus	2021-02-12 11:51:24 -08:00
Anders Goncalves da Silva	bfc13d3379	Add options to make samtools more flexible	2021-02-12 11:50:33 -08:00
Anders Goncalves da Silva	a4bba006bd	Add reference fasta as input	2021-02-12 11:26:55 -08:00
Anders Goncalves da Silva	6b22bb9782	Add meta.yml	2021-02-12 11:25:40 -08:00
JoseEspinosa	0688230863	Revert since fixes to test were not working ... This reverts commit d7a219e88d.	2021-02-12 18:02:32 +01:00
JoseEspinosa	8e23e1839d	Trying to fix tests	2021-02-12 17:56:51 +01:00
JoseEspinosa	6e8b63fc26	Add cat fastq module	2021-02-12 17:22:07 +01:00
Maxime Garcia	27be87ac72	Merge pull request #135 from drpatelh/bwa ... Update indices syntax for BWA index and mem modules	2021-02-12 12:45:38 +01:00
Anders Goncalves da Silva	e9aa037e7b	Add function to enable output of mpileup ... Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>	2021-02-10 10:02:06 -08:00
Anders Goncalves da Silva	06770d5f02	Specify the exact bioconda recipe build ... Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>	2021-02-10 10:01:25 -08:00
Anders Goncalves da Silva	362a630f8b	Change suffix of mpileup ouput file ... Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>	2021-02-10 10:00:54 -08:00
Anders Goncalves da Silva	884c4658b8	Make mpileup saving optional ... Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>	2021-02-10 10:00:22 -08:00
Jose Espinosa-Carrasco	1e771ac8a0	Merge pull request #164 from drpatelh/fixes ... Add missing build ids and rename *.txt channels	2021-02-10 14:19:00 +01:00
drpatelh	b9afca2b05	Underscore not .	2021-02-10 12:53:17 +00:00
drpatelh	d2508e3c03	Amend prefix for bcftools stats	2021-02-10 12:51:47 +00:00
drpatelh	e63279e6a2	Pin pangoLearn version	2021-02-10 10:28:27 +00:00
drpatelh	b03846600d	Tidy up	2021-02-09 23:26:45 +00:00
drpatelh	6795fe04b8	Rename output channel	2021-02-09 23:26:18 +00:00
drpatelh	2b9129b3f9	Change txt channel output	2021-02-09 23:09:22 +00:00
drpatelh	d50d070c06	Change txt channel output	2021-02-09 23:09:18 +00:00
drpatelh	0b33b6d081	Add missing build ids	2021-02-09 23:03:13 +00:00
JoseEspinosa	e8dc199dc8	Adding conda build to blast modules	2021-02-09 23:04:12 +01:00
JoseEspinosa	2fa14f2ec8	Adding conda build to bcftools modules	2021-02-09 23:00:19 +01:00
Harshil Patel	3f431014a4	Update software/bedtools/getfasta/main.nf	2021-02-09 21:34:40 +00:00
Anders Goncalves da Silva	8f546a1f95	Add ivar consensus	2021-02-09 10:26:35 -08:00
JoseEspinosa	68b85d9191	Merge remote-tracking branch 'upstream/master' into bedtools_getfasta	2021-02-09 18:23:24 +01:00
JoseEspinosa	e118bc049a	Add bedtools getfasta module	2021-02-09 17:56:51 +01:00
JoseEspinosa	12ae7b0bff	Adding blast blastn module	2021-02-09 16:58:36 +01:00
JoseEspinosa	c23b355b35	Add blast makeblastdb module	2021-02-09 15:44:34 +01:00