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Author	SHA1	Message	Date
Anders Goncalves da Silva	4ab3ccc905	Add ivar variants	2021-02-15 09:28:10 -08:00
Anders Goncalves da Silva	2fe3210f88	Add ivar variants	2021-02-15 09:27:59 -08:00
Maxime Garcia	b28604efca	Merge pull request #166 from MaxUlysse/master_bwa-mem2 ... chores: add bwa-mem2 index + mem	2021-02-15 18:14:50 +01:00
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	3d53917b47	Merge pull request #170 from andersgs/ivar_trim ... Add ivar trim	2021-02-13 08:24:12 +00:00
Harshil Patel	4af9417b6d	Update software/ivar/trim/main.nf	2021-02-13 08:20:06 +00:00
Harshil Patel	a5686ed14e	Update software/ivar/trim/main.nf	2021-02-13 08:19:55 +00:00
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	25f3d46f68	Update software/ivar/trim/meta.yml	2021-02-13 08:17:03 +00:00
Harshil Patel	cdd9be0a2d	Update tests/software/ivar/trim/main.nf	2021-02-13 08:16:44 +00:00
Anders Goncalves da Silva	bbdca4fa76	Fix output files	2021-02-12 16:14:46 -08:00
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	7c9766962d	Add ivar trim meta.yml	2021-02-12 16:02:48 -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
Harshil Patel	b74ba0af1e	Merge pull request #162 from andersgs/ivar-consensus ... Add ivar consensus module	2021-02-12 23:18:57 +00:00
Harshil Patel	c0d128fd39	Update software/bcftools/merge/main.nf	2021-02-12 23:16:52 +00:00
Anders Goncalves da Silva	9268851cde	Remove samtools option ... Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>	2021-02-12 15:09:50 -08:00
Anders Goncalves da Silva	1f66954180	Relabel input parameter ... Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>	2021-02-12 15:09:35 -08:00
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
Harshil Patel	0580fd8ded	Update software/ivar/consensus/main.nf	2021-02-12 23:02:04 +00:00
Harshil Patel	9e4539473e	Update software/ivar/consensus/main.nf	2021-02-12 23:01:53 +00:00
Harshil Patel	bc5e073cdb	Update software/ivar/consensus/main.nf	2021-02-12 22:57:06 +00:00
Anders Goncalves da Silva	cb19c7b056	Fix trailing whitespace	2021-02-12 14:46:13 -08:00
Anders Goncalves da Silva	b08bf1ea5c	Remove ref to conda build and additional params	2021-02-12 14:43:50 -08:00
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	bfc13d3379	Add options to make samtools more flexible	2021-02-12 11:50:33 -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
Anders Goncalves da Silva	a4bba006bd	Add reference fasta as input	2021-02-12 11:26:55 -08:00
Anders Goncalves da Silva	6b22bb9782	Add meta.yml	2021-02-12 11:25:40 -08:00
Anders Goncalves da Silva	e5a3e3a5b8	Add ivar consensus to filter.yml	2021-02-12 10:59:46 -08:00
Harshil Patel	0b5b8957f4	Merge pull request #167 from JoseEspinosa/cat_fastq ... Add cat fastq module	2021-02-12 18:02:10 +00:00
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
MaxUlysse	2f18750964	chores: update filters.yml	2021-02-12 13:53:49 +01:00
Maxime Garcia	c1ff201518	Apply suggestions from code review ... Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>	2021-02-12 13:24:10 +01:00
MaxUlysse	6b34ddf239	chores: bwa-mem2 -> bwamem2	2021-02-12 13:08:44 +01:00