231 commits

Author	SHA1	Message	Date
Anders Goncalves da Silva	ffa9cf85b1	Clean up header params ... I used these for testing and forgot to remove them Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>	2021-02-10 12:03:50 -08:00
Anders Goncalves da Silva	1f6419f8f5	Fix indentation ... Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>	2021-02-10 10:55:24 -08:00
Anders Goncalves da Silva	8f546a1f95	Add ivar consensus	2021-02-09 10:26:35 -08:00
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	9b65961828	Fix file output path on test	2021-02-09 10:22:50 +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
Harshil Patel	132dabbbb6	Update tests/data/bed/C.bed	2021-02-08 23:03:26 +00:00
JoseEspinosa	1b3e5e0283	Fixing module name in test.yml	2021-02-08 23:45:01 +01:00
JoseEspinosa	02d10c25a3	Add bedtools maskfasta module	2021-02-08 23:41:10 +01:00
drpatelh	0b9e32e32d	Remove complement suffix from tests	2021-02-08 22:25:13 +00:00
Harshil Patel	0f6830f7cc	Update tests/software/bcftools/consensus/main.nf	2021-02-08 21:41:24 +00:00
JoseEspinosa	f8882de456	Renaming test ymls just to: software tool	2021-02-08 21:56:53 +01:00
JoseEspinosa	f4e322f88d	Merging upstream changes ... # Conflicts: # .github/filters.yml	2021-02-08 18:09:41 +01:00
JoseEspinosa	4fa38ebb7a	Separate test data to break dependencies between bcftools modules tests	2021-02-08 16:51:21 +01:00
JoseEspinosa	83cc25860d	Rearranging tests to test each module separately	2021-02-08 15:16:51 +01:00
JoseEspinosa	5071bf5914	Merge remote-tracking branch 'upstream/master' into bcftools_viralrecon	2021-02-08 10:45:57 +01:00
drpatelh	83a50d8ae0	Rename SOFTWARE_TOOL to TOOL_SUBTOOL	2021-02-07 23:20:53 +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
Harshil Patel	0393d39105	Update tests/software/bedtools/complement/main.nf	2021-02-07 20:35:51 +00:00
Harshil Patel	5269c1ec60	Update tests/software/bedtools/intersect/main.nf	2021-02-07 20:35:12 +00:00
Harshil Patel	8841af1267	Update tests/software/bedtools/merge/main.nf	2021-02-07 20:34:30 +00:00
Harshil Patel	b068f2fc53	Update tests/software/bedtools/sort/main.nf	2021-02-07 20:33:02 +00:00
JoseEspinosa	26829497d5	Fixing typo on path for md5 check	2021-02-02 12:19:57 +01:00
JoseEspinosa	e7f15feccf	Adding --no-version to bcftools_isec for tests md5 check	2021-02-02 11:00:02 +01:00
JoseEspinosa	3a40ec5664	Adding bcftools_isec taking a path with several vcfs and its tests	2021-02-02 10:50:45 +01:00
JoseEspinosa	8e4764b8ed	bcftools_filter adding argument to test to enable md5 check	2021-02-02 10:19:34 +01:00
JoseEspinosa	c25f8f0f6c	Fixing tests	2021-02-02 09:57:55 +01:00
JoseEspinosa	382ea31e7e	Adding bcftools test data	2021-02-02 09:18:28 +01:00
JoseEspinosa	cee37852cd	Merge remote-tracking branch 'upstream/master' into bcftools_viralrecon	2021-02-02 09:15:20 +01:00
JoseEspinosa	a3ce63c79c	Adding tests for bcftools	2021-02-02 09:14:00 +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	0bd8506ea1	Update tests/software/quast/main.nf ... Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>	2021-02-01 14:04:08 +01:00
Kevin Menden	05370b5e16	Update tests/software/quast/main.nf ... Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>	2021-02-01 14:03:49 +01:00
kevinmenden	e9e795633d	added fastp tests	2021-02-01 14:02:06 +01:00
kevinmenden	a342296d70	fixed test md5s	2021-02-01 13:36:25 +01:00
kevinmenden	b5298f94d8	refactored quast module	2021-02-01 13:13:21 +01:00
Harshil Patel	c74d8a1711	Merge pull request #128 from JoseEspinosa/bowtie2_viralrecon ... Bowtie2 viralrecon 2	2021-02-01 09:56:11 +00:00
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	8fb6b80abd	Fixing some md5 hashes	2021-01-30 23:08:17 +01:00