240 commits

Author	SHA1	Message	Date
phue	5ad7c6bc51	add methyldackel/extract + tests + testdata	2021-02-17 19:18:55 +01:00
Maxime Garcia	842173be9f	Merge pull request #175 from MaxUlysse/master_ISSUE_TEMPLATE ... fix: add guidelines to PRs and issues	2021-02-17 00:36:35 +01:00
MaxUlysse	ebb6d5de1f	fix: Apply suggestions from code review	2021-02-17 00:34:55 +01:00
Harshil Patel	412172cda6	Merge pull request #180 from MaxUlysse/master_tabix_bgzip ... Replace bcftools/bgzip by tabix/bgzip	2021-02-16 23:32:23 +00:00
Maxime Garcia	75d1483417	Apply suggestions from code review ... Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>	2021-02-17 00:32:06 +01:00
Harshil Patel	a282ecd8c7	Merge pull request #172 from andersgs/ivar-variant ... Add ivar variants	2021-02-16 23:20:30 +00:00
Harshil Patel	b07ad23efa	Merge pull request #179 from MaxUlysse/master_htslib_tabix ... Replace bcftools/tabix by tabix/tabix	2021-02-16 22:30:45 +00:00
Harshil Patel	759079796a	Update .github/filters.yml	2021-02-16 22:24:49 +00:00
MaxUlysse	6a147b8aaa	chores: replace bcftools/bgzip by tabix/bgzip cf #179	2021-02-16 19:11:36 +01:00
MaxUlysse	3805eb2dd1	fix: remove bcftools/tabix from filters.yml	2021-02-16 18:38:20 +01:00
MaxUlysse	10524e3515	chores: add modules for htslib/tabix	2021-02-16 14:47:53 +01:00
MaxUlysse	bbee0efd75	fix: add suggestions from reviews	2021-02-16 13:59:21 +01:00
MaxUlysse	7f35a1742d	chores: add gatk/createsequencedictionary module	2021-02-16 13:40:06 +01:00
MaxUlysse	a285bfe8a6	fix: add guidelines to PRs and issues	2021-02-16 11:07:43 +01:00
Anders Goncalves da Silva	89f65e0875	Merge branch 'master' into ivar-variant	2021-02-15 20:50:35 -08:00
Harshil Patel	8eb3acc43f	Merge pull request #171 from JoseEspinosa/mosdepth ... Add mosdepth module	2021-02-15 23:13:01 +00:00
Anders Goncalves da Silva	4ab3ccc905	Add ivar variants	2021-02-15 09:28:10 -08:00
JoseEspinosa	6e92a6a080	Adding mosdepth module	2021-02-15 14:33:44 +01:00
Maxime Garcia	ec0bf0145e	Merge branch 'master' into master_bwa-mem2	2021-02-15 13:08:52 +01:00
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
JoseEspinosa	5313698705	Add bcftools merge module	2021-02-13 00:08:57 +01:00
Anders Goncalves da Silva	24b212318b	Merge branch 'master' into ivar-consensus	2021-02-12 11:51:24 -08:00
Anders Goncalves da Silva	e5a3e3a5b8	Add ivar consensus to filter.yml	2021-02-12 10:59:46 -08:00
JoseEspinosa	6e8b63fc26	Add cat fastq module	2021-02-12 17:22:07 +01:00
MaxUlysse	2f18750964	chores: update filters.yml	2021-02-12 13:53:49 +01:00
JoseEspinosa	68b85d9191	Merge remote-tracking branch 'upstream/master' into bedtools_getfasta	2021-02-09 18:23:24 +01:00
JoseEspinosa	1e9b88b33c	Fixing trailing slashes in .github/filters.yml	2021-02-09 18:16:16 +01:00
JoseEspinosa	e118bc049a	Add bedtools getfasta module	2021-02-09 17:56:51 +01:00
JoseEspinosa	9a11e90892	Fixing tests	2021-02-09 17:07:23 +01:00
JoseEspinosa	12ae7b0bff	Adding blast blastn module	2021-02-09 16:58:36 +01:00
JoseEspinosa	d0f09e26b6	Adding blast makeblastdb module to filters.yml	2021-02-09 15:47:53 +01:00
JoseEspinosa	c93e96101a	Add untar module	2021-02-09 11:50:32 +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
Harshil Patel	13c1e908a3	Update .github/filters.yml	2021-02-08 21:48:21 +00:00
JoseEspinosa	58d28ed896	Fix copy/paste error :P	2021-02-08 21:57:31 +01:00
JoseEspinosa	7a0ba85843	Adding again bcftools modules to filters after solving conflict	2021-02-08 18:10:50 +01:00
drpatelh	c9cfdd31f3	Fix barfing linters	2021-02-08 00:57:06 +00:00
drpatelh	eeb496cf5c	Fix filters	2021-02-07 23:23:08 +00:00
drpatelh	83a50d8ae0	Rename SOFTWARE_TOOL to TOOL_SUBTOOL	2021-02-07 23:20:53 +00:00
drpatelh	418bd64e80	Test module with Conda	2021-02-07 21:33:42 +00:00
sruthipsuresh	93e414635b	Fixed md5sum, fixed filters, fixed slop input	2021-01-29 23:17:44 -06:00
sruthipsuresh	ac7f634675	Added complement test	2021-01-29 23:17:44 -06:00
sruthipsuresh	84b66e4f38	Fixed testing, rebased	2021-01-29 23:17:44 -06:00
sruthipsuresh	70de0331a5	Corrected pytest and config	2021-01-29 23:17:44 -06:00
sruthipsuresh	32564137fd	Corrected workflows and ran editor config	2021-01-29 23:17:44 -06:00
sruthipsuresh	672f94f2af	rebased and updated all bedtools testing and modules	2021-01-29 23:17:44 -06:00