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Author	SHA1	Message	Date
Harshil Patel	759079796a	Update .github/filters.yml	2021-02-16 22:24:49 +00:00
MaxUlysse	3805eb2dd1	fix: remove bcftools/tabix from filters.yml	2021-02-16 18:38:20 +01:00
MaxUlysse	5a144d6213	fix: merge bcftools/tabix and htslib/tabix tests into tabix/tabix	2021-02-16 18:35:32 +01:00
MaxUlysse	edf5fa3cf6	fix: merge bcftools/tabix and htslib/tabix into tabix/tabix	2021-02-16 18:27:13 +01:00
MaxUlysse	f660324508	chores: move file	2021-02-16 18:20:43 +01:00
MaxUlysse	274897f1fd	fix: ECLint: Wrong line endings or new final newline	2021-02-16 17:11:50 +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
MaxUlysse	3da905b0fd	chores: remove deprecated module	2021-02-16 14:31:16 +01:00
Harshil Patel	7d5ac60aa1	Merge pull request #176 from nf-core/MaxUlysse-patch-1 ... Update meta.yml	2021-02-16 10:43:18 +00:00
Maxime Garcia	d8706c12b3	Update meta.yml ... typo	2021-02-16 11:22:15 +01:00
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
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