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Author	SHA1	Message	Date
Anders Goncalves da Silva	b99972f3a0	Move params to nextflow invocation	2021-02-15 20:59:45 -08:00
Anders Goncalves da Silva	89f65e0875	Merge branch 'master' into ivar-variant	2021-02-15 20:50:35 -08:00
Anders Goncalves da Silva	7cae9b1842	Add gff to meta yaml	2021-02-15 20:49:37 -08:00
Anders Goncalves da Silva	c12a558f15	Add tests without mpileup	2021-02-15 20:49:27 -08:00
Anders Goncalves da Silva	26189f4132	Change ternary expressions back to traditional format ... Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>	2021-02-15 19:56:22 -08:00
Anders Goncalves da Silva	3188b8e30e	Add explicit gff is false param ... Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>	2021-02-15 19:55:34 -08:00
Anders Goncalves da Silva	ee4c2828a0	Update gff assignment to string ... Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>	2021-02-15 19:55:12 -08:00
Anders Goncalves da Silva	39401ccd07	Add gff as input ... Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>	2021-02-15 19:54:36 -08:00
Anders Goncalves da Silva	8b6989f2d7	Add gff as input ... Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>	2021-02-15 19:54:19 -08:00
Anders Goncalves da Silva	4f8ab8bd69	Rename gff to features ... Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>	2021-02-15 19:53:30 -08:00
Anders Goncalves da Silva	8c483d4c6a	Add gff as input for proper staging ... Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>	2021-02-15 19:53:13 -08:00
Anders Goncalves da Silva	6259b72081	Fix output format ... Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>	2021-02-15 19:52:30 -08:00
Anders Goncalves da Silva	ef1e1b2539	Fix indentation ... Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>	2021-02-15 19:51:45 -08:00
Harshil Patel	8eb3acc43f	Merge pull request #171 from JoseEspinosa/mosdepth ... Add mosdepth module	2021-02-15 23:13:01 +00:00
Harshil Patel	f97c78b3fb	Update software/mosdepth/main.nf	2021-02-15 22:49:53 +00:00
Anders Goncalves da Silva	f841483a70	Fix URL for containers	2021-02-15 13:23:35 -08:00
Anders Goncalves da Silva	9a5aa0f145	Fix tests to work with gff param	2021-02-15 11:51:04 -08:00
Anders Goncalves da Silva	e8d1171b5d	Make gff a param and not an optional input	2021-02-15 11:50:52 -08:00
Anders Goncalves da Silva	4af7414419	Add tests for ivar variants	2021-02-15 09:29:40 -08:00
Anders Goncalves da Silva	9e3c4e598c	Add meta to ivar variants	2021-02-15 09:29:10 -08:00
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