260 commits

Author	SHA1	Message	Date
Anders Goncalves da Silva	ffc849761d	Edit test to output mpileup and passing args to samtools	2021-02-12 14:43:19 -08:00
Anders Goncalves da Silva	487ec7b793	Fix test.yml	2021-02-12 14:42:42 -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	8b3c16a518	Add ref FASTA to test main.nf	2021-02-12 11:29:16 -08:00
Anders Goncalves da Silva	0a6e8400ac	Add reference SC2 genome to test data	2021-02-12 11:27:12 -08:00
JoseEspinosa	fafe068192	Fixing test tags	2021-02-12 18:49:57 +01:00
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	d7a219e88d	Fix test.yml	2021-02-12 17:37:49 +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	df9125b46a	Fix test name ... Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>	2021-02-10 12:05:01 -08:00
Anders Goncalves da Silva	40bbf94ef9	Update filename for outputted mpileup file in test ... Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>	2021-02-10 12:04:46 -08:00
Anders Goncalves da Silva	68de6fef0d	Fix indentation ... Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>	2021-02-10 12:04:15 -08:00
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
drpatelh	1d00a4a11c	Update md5sum	2021-02-09 23:31:39 +00:00
drpatelh	79d730f2c3	Change output name	2021-02-09 23:27:08 +00:00
drpatelh	7f629bca45	OCDness	2021-02-09 23:26:55 +00:00
Harshil Patel	28866f3dc7	Update tests/software/bedtools/maskfasta/main.nf	2021-02-09 21:36:38 +00:00
Harshil Patel	aaa088dba8	Update tests/software/bedtools/getfasta/main.nf	2021-02-09 21:34:29 +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	7536b386a5	Correct channel declaration on bedtools_maskfasta	2021-02-09 17:56:01 +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	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