279 commits

Author	SHA1	Message	Date
MaxUlysse	f660324508	chores: move file	2021-02-16 18:20:43 +01:00
MaxUlysse	5e71dc94d6	fix: make HTSLIB_TABIX more modular	2021-02-16 17:06:55 +01:00
MaxUlysse	fa34f806d2	chores: add bgzip files for tests	2021-02-16 17:06:09 +01:00
MaxUlysse	10524e3515	chores: add modules for htslib/tabix	2021-02-16 14:47:53 +01:00
Harshil Patel	8eb3acc43f	Merge pull request #171 from JoseEspinosa/mosdepth ... Add mosdepth module	2021-02-15 23:13:01 +00:00
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
Harshil Patel	f51f8c6400	Update tests/software/ivar/trim/main.nf	2021-02-13 08:18:32 +00:00
Harshil Patel	9d6f29fc61	Update tests/software/ivar/trim/main.nf	2021-02-13 08:17:15 +00:00
Harshil Patel	cdd9be0a2d	Update tests/software/ivar/trim/main.nf	2021-02-13 08:16:44 +00:00
Anders Goncalves da Silva	47670a12ad	Fix ivar trim test.yml	2021-02-12 16:03:18 -08:00
Anders Goncalves da Silva	ed74d366bf	Clean up ivar trim main.nf	2021-02-12 16:03:07 -08:00
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
Harshil Patel	96d3b0a18b	Update tests/software/ivar/consensus/main.nf	2021-02-12 23:02:25 +00:00
Harshil Patel	f8916060f8	Update tests/software/ivar/consensus/main.nf	2021-02-12 23:02:19 +00:00
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
MaxUlysse	9c98194d3c	chores: remove fasta file from bwamem2 mem process	2021-02-12 16:00:59 +01:00
MaxUlysse	0afddf6ca4	fix: CI is working	2021-02-12 15:24:09 +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