392 commits

Author	SHA1	Message	Date
MaxUlysse	6b34ddf239	chores: bwa-mem2 -> bwamem2	2021-02-12 13:08:44 +01:00
MaxUlysse	a910d1a608	chores: add bwa-mem2 index + mem	2021-02-12 13:00:02 +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
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
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
JoseEspinosa	c93e96101a	Add untar module	2021-02-09 11:50:32 +01:00
JoseEspinosa	20771ae1bc	Remove meta from input/output meta.yml	2021-02-09 11:02:31 +01:00
JoseEspinosa	b09416a0d0	Correcting meta.yml	2021-02-09 10:51:57 +01:00
JoseEspinosa	f7f06dd6e8	Add gunzip module	2021-02-09 10:05:55 +01:00
Harshil Patel	46e5df2cf7	Merge pull request #151 from drpatelh/bedtools ... Follow up fixes for bedtools modules added in #79	2021-02-09 01:54:31 +00:00
Harshil Patel	84cf5ea2ef	Merge pull request #153 from JoseEspinosa/bedtools_maskfasta ... Add bedtools maskfasta module	2021-02-08 23:11:00 +00:00
JoseEspinosa	02d10c25a3	Add bedtools maskfasta module	2021-02-08 23:41:10 +01:00
JoseEspinosa	f4e322f88d	Merging upstream changes ... # Conflicts: # .github/filters.yml	2021-02-08 18:09:41 +01:00
JoseEspinosa	fe412797dd	Adressing general comments on PR #134	2021-02-08 15:11:36 +01:00
JoseEspinosa	5071bf5914	Merge remote-tracking branch 'upstream/master' into bcftools_viralrecon	2021-02-08 10:45:57 +01:00
drpatelh	c9cfdd31f3	Fix barfing linters	2021-02-08 00:57:06 +00:00
drpatelh	83a50d8ae0	Rename SOFTWARE_TOOL to TOOL_SUBTOOL	2021-02-07 23:20:53 +00:00
drpatelh	a34d74188d	Really fix Editor Config	2021-02-07 21:49:20 +00:00
drpatelh	ef0a984cc0	Fix Editor config tests	2021-02-07 21:44:45 +00:00
drpatelh	5779b180da	Fix bedtools sort module	2021-02-07 21:32:43 +00:00
drpatelh	f3b5af4ed5	Fix bedtools slip module	2021-02-07 21:32:20 +00:00
drpatelh	38964ecfc0	Fix bedtools intersect module	2021-02-07 21:32:01 +00:00
drpatelh	a37b116186	Fix bedtools merge module	2021-02-07 21:31:39 +00:00
drpatelh	4564ef0e54	Fix bedtools genomecov module	2021-02-07 21:31:21 +00:00
drpatelh	a0c08e0c06	Fix bedtools complement module	2021-02-07 21:31:02 +00:00
drpatelh	a9102c329c	Fix bedtools complement module	2021-02-07 20:55:12 +00:00
drpatelh	81ae0089bc	Fix merge conflicts	2021-02-05 10:06:39 +00:00
Michael L Heuer	37a9f6f456	Address review comments	2021-02-04 12:10:54 -06:00
Kevin Menden	f298c594fe	Update meta.yml ... Just a small edit, we want to keep this consistent for linting	2021-02-04 07:34:08 +01:00
Michael L Heuer	05d257e8f5	Fix lint errors	2021-02-03 19:34:25 -06:00
Michael L Heuer	c466255f6f	Add bandage image module	2021-02-03 19:31:58 -06:00
drpatelh	673d463208	bowtie - add mulled build info	2021-02-03 11:33:31 +00:00
drpatelh	423144808c	seacr - add build info for mulled container	2021-02-03 11:05:10 +00:00
drpatelh	34e451dd2e	rsem - add build info for mulled container	2021-02-03 11:04:59 +00:00
drpatelh	26e04dd298	rsem - add build info for mulled container	2021-02-03 11:04:51 +00:00
drpatelh	3d1b9371f2	hisat2 - add build info for mulled container	2021-02-03 11:04:35 +00:00