365 commits

Author	SHA1	Message	Date
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
JoseEspinosa	3a40ec5664	Adding bcftools_isec taking a path with several vcfs and its tests	2021-02-02 10:50:45 +01:00
JoseEspinosa	c25f8f0f6c	Fixing tests	2021-02-02 09:57:55 +01:00
JoseEspinosa	cee37852cd	Merge remote-tracking branch 'upstream/master' into bcftools_viralrecon	2021-02-02 09:15:20 +01:00
JoseEspinosa	579de3e038	bcftools_tabix generic for any TAB-delimited genome position file	2021-02-01 21:59:39 +01:00
drpatelh	f84e5b59ca	Rename bowtie_index to bowtie_build	2021-02-01 17:53:31 +00:00
Harshil Patel	0a41130276	Merge pull request #131 from KevinMenden/fastp-module ... Adding fastp module	2021-02-01 13:43:35 +00:00
Harshil Patel	e851da8640	Merge pull request #130 from KevinMenden/master ... Adding a QUAST module	2021-02-01 13:17:57 +00:00
Kevin Menden	f6c4e9d9c1	Update software/quast/meta.yml ... Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>	2021-02-01 14:03:36 +01:00
Kevin Menden	9885da628e	Update software/quast/meta.yml ... Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>	2021-02-01 14:03:22 +01:00
Kevin Menden	c807c6c438	Update software/quast/main.nf ... Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>	2021-02-01 14:03:15 +01:00
Kevin Menden	d88bf3bdda	Update software/quast/main.nf ... Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>	2021-02-01 14:03:06 +01:00
Kevin Menden	c43fe85a0c	Update software/quast/main.nf ... Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>	2021-02-01 14:02:57 +01:00
kevinmenden	038381de99	added fastp module	2021-02-01 13:54:08 +01:00
kevinmenden	b5298f94d8	refactored quast module	2021-02-01 13:13:21 +01:00
Harshil Patel	2c962f34df	Merge pull request #110 from luslab/master ... Add SEACR module containing a single CALLPEAK process	2021-02-01 09:48:15 +00:00
JoseEspinosa	0a8915ae77	Adding bcftools_tabix module	2021-02-01 10:07:35 +01:00
JoseEspinosa	52b0b8094d	Adding bcftools_stats module	2021-02-01 10:03:25 +01:00
JoseEspinosa	0423e686a6	Adding bcftools_isec module	2021-02-01 09:46:24 +01:00
JoseEspinosa	da7598272e	Adding bcftools_filter module	2021-02-01 09:41:08 +01:00
JoseEspinosa	eb12f4610d	Fixing meta ymls	2021-02-01 09:28:51 +01:00
kevinmenden	956bf22a58	fixed bug; updated meta.yml	2021-02-01 07:44:26 +01:00
JoseEspinosa	b6ef06c6cd	Add bcftools_consensus module	2021-01-31 22:23:26 +01:00
Harshil Patel	eadbea4b83	Merge pull request #127 from JoseEspinosa/bowtie2_viralrecon ... Bowtie2 viralrecon	2021-01-30 13:22:30 +00:00
Harshil Patel	eab633776e	Update software/bowtie2/build/meta.yml	2021-01-30 13:21:56 +00:00
JoseEspinosa	500481833f	Adding bcftools_bgzip module	2021-01-30 11:22:25 +01:00
JoseEspinosa	986b72cee9	Fix error on previous commit	2021-01-30 09:35:25 +01:00
JoseEspinosa	29989035a5	Remove author entry from yml (copy-pasted :P)	2021-01-30 09:29:53 +01:00
sruthipsuresh	e360617ac6	Fixed images, genomecov	2021-01-29 23:17:44 -06:00
sruthipsuresh	e3bbbb48fc	Fixed slop file	2021-01-29 23:17:44 -06:00
sruthipsuresh	957983bd99	Fixed and tested 4 modules, keeping with fastp module syntax	2021-01-29 23:17:44 -06:00
sruthipsuresh	295fff35ec	Corrected containers and tested	2021-01-29 23:17:44 -06:00
sruthipsuresh	19b55fc67c	Fixed intersect, complement indentation issues	2021-01-29 23:17:44 -06:00