273 commits

Author	SHA1	Message	Date
Patrick Hüther	0cbe0a4173	Update tests/software/samtools/faidx/main.nf ... Co-authored-by: Maxime Garcia <maxime.garcia@scilifelab.se>	2021-02-17 17:24:50 +01:00
phue	3b1d126a0e	add samtools/faidx + tests	2021-02-17 16:46:34 +01:00
Harshil Patel	ed573db194	Merge pull request #184 from MaxUlysse/master_fix_ci ... fix: update checksum or filename	2021-02-17 10:54:38 +00:00
Harshil Patel	4d656c8f5f	Merge pull request #181 from drpatelh/fixes ... Fix tests for iVar variants	2021-02-17 10:08:57 +00:00
MaxUlysse	28fb5e8cbd	fix: update checksum or filename	2021-02-17 01:34:50 +01:00
Harshil Patel	412172cda6	Merge pull request #180 from MaxUlysse/master_tabix_bgzip ... Replace bcftools/bgzip by tabix/bgzip	2021-02-16 23:32:23 +00:00
drpatelh	c6a0976f52	Fix tests for iVar variants	2021-02-16 23:29:15 +00:00
MaxUlysse	596bb18394	fix: rename file to input and gz, plus fix tests	2021-02-17 00:28:32 +01:00
Harshil Patel	a282ecd8c7	Merge pull request #172 from andersgs/ivar-variant ... Add ivar variants	2021-02-16 23:20:30 +00:00
Harshil Patel	cf2f0762aa	Update main.nf	2021-02-16 23:06:26 +00:00
Harshil Patel	7c276d2974	Update tests/software/ivar/variants/main.nf	2021-02-16 23:01:27 +00:00
Harshil Patel	27020105aa	Update tests/software/ivar/variants/main.nf	2021-02-16 23:00:30 +00:00
Harshil Patel	de90d371dc	Update tests/software/ivar/variants/main.nf	2021-02-16 22:58:38 +00:00
Harshil Patel	23987bdad0	Update tests/software/ivar/variants/main.nf	2021-02-16 22:57:47 +00:00
Harshil Patel	b07ad23efa	Merge pull request #179 from MaxUlysse/master_htslib_tabix ... Replace bcftools/tabix by tabix/tabix	2021-02-16 22:30:45 +00:00
Harshil Patel	4f11064ae2	Update tests/software/tabix/bgzip/main.nf	2021-02-16 22:30:06 +00:00
Harshil Patel	8dd6d1d38a	Update tests/software/tabix/bgzip/main.nf	2021-02-16 22:29:13 +00:00
MaxUlysse	6a147b8aaa	chores: replace bcftools/bgzip by tabix/bgzip cf #179	2021-02-16 19:11:36 +01:00
MaxUlysse	5a144d6213	fix: merge bcftools/tabix and htslib/tabix tests into tabix/tabix	2021-02-16 18:35:32 +01:00
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	10524e3515	chores: add modules for htslib/tabix	2021-02-16 14:47:53 +01:00
MaxUlysse	763800a0e2	fix: correct md5sum	2021-02-16 13:54:54 +01:00
MaxUlysse	7f35a1742d	chores: add gatk/createsequencedictionary module	2021-02-16 13:40:06 +01:00
Anders Goncalves da Silva	eeedb959c9	Clean out comments	2021-02-15 21:04:17 -08:00
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	c12a558f15	Add tests without mpileup	2021-02-15 20:49:27 -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
Harshil Patel	8eb3acc43f	Merge pull request #171 from JoseEspinosa/mosdepth ... Add mosdepth module	2021-02-15 23:13:01 +00:00
Anders Goncalves da Silva	9a5aa0f145	Fix tests to work with gff param	2021-02-15 11:51:04 -08:00
Anders Goncalves da Silva	4af7414419	Add tests for ivar variants	2021-02-15 09:29:40 -08:00
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