468 commits

Author	SHA1	Message	Date
FriederikeHanssen	bf58948dad	remove todos, describe in/output	2021-02-23 15:41:11 +01:00
FriederikeHanssen	4e9d728108	allow fq.gz or gastq.gz as in/output	2021-02-23 15:40:22 +01:00
FriederikeHanssen	12137d6f3e	Remove trialing whitespace	2021-02-23 15:00:21 +01:00
FriederikeHanssen	e251a3bed5	Remove todos	2021-02-23 14:58:09 +01:00
FriederikeHanssen	13733b2581	Add beautiful md5sums	2021-02-23 14:57:07 +01:00
FriederikeHanssen	5e365d5eff	Make all these tests pass	2021-02-23 14:09:46 +01:00
FriederikeHanssen	25a2a16f2d	Try to make a single test pass	2021-02-23 13:34:50 +01:00
FriederikeHanssen	2654c52ed1	Use list of reads as input, similar to dedup/extract	2021-02-17 17:15:02 +01:00
FriederikeHanssen	bedc2972eb	Add seqkit split2	2021-02-17 17:09:24 +01:00
drpatelh	d47f9bb909	@kevinmenden sanity fix	2021-02-16 23:58:52 +00:00
drpatelh	dcc580e4fb	Remove Conda build ids for all modules	2021-02-16 23:58:23 +00:00
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
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	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	d6d34a4b5b	Merge pull request #177 from MaxUlysse/master_gatk_createsequencedictionary ... Add gatk/createsequencedictionary	2021-02-16 22:21:38 +00:00
Harshil Patel	a6d6c0b973	Update software/gatk/createsequencedictionary/main.nf	2021-02-16 22:08:11 +00:00
Harshil Patel	7c64e70c9e	Update software/gatk/createsequencedictionary/meta.yml	2021-02-16 22:07:51 +00:00
Harshil Patel	e558d5fb57	Merge pull request #174 from andersgs/ivar_consensus_fix ... ivar consensus: Add save mpileup as optional in output directive	2021-02-16 22:04:38 +00:00
MaxUlysse	6a147b8aaa	chores: replace bcftools/bgzip by tabix/bgzip cf #179	2021-02-16 19:11:36 +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	10524e3515	chores: add modules for htslib/tabix	2021-02-16 14:47:53 +01:00
MaxUlysse	28dc9227d7	fix: remove memory requirements and simplify URI	2021-02-16 13:54:40 +01:00
MaxUlysse	30e3f2c5f5	fix: ECLint check: trailing whitespace	2021-02-16 13:42:34 +01:00
MaxUlysse	7f35a1742d	chores: add gatk/createsequencedictionary module	2021-02-16 13:40:06 +01:00
Maxime Garcia	d8706c12b3	Update meta.yml ... typo	2021-02-16 11:22:15 +01:00
Anders Goncalves da Silva	fd854c333e	Add save mpileup as optional in output directive	2021-02-15 21:07:31 -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	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	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	e8d1171b5d	Make gff a param and not an optional input	2021-02-15 11:50:52 -08:00
Anders Goncalves da Silva	9e3c4e598c	Add meta to ivar variants	2021-02-15 09:29:10 -08:00
Anders Goncalves da Silva	2fe3210f88	Add ivar variants	2021-02-15 09:27:59 -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	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	25f3d46f68	Update software/ivar/trim/meta.yml	2021-02-13 08:17:03 +00:00
Anders Goncalves da Silva	bbdca4fa76	Fix output files	2021-02-12 16:14:46 -08:00
Anders Goncalves da Silva	7c9766962d	Add ivar trim meta.yml	2021-02-12 16:02:48 -08:00