514 commits

Author	SHA1	Message	Date
Kevin Menden	a552d97849	Exchange VCF data by sarscov2 data (#261) ... * added sarscov2 vcf data; adjusted bcftools tests * updated README.md * deleted old VCF files; fixed mergevcfs * fixed tabix	2021-03-09 10:04:08 +01:00
Maxime Garcia	05cbbbaded	Rename gatk/createsequencedictionary -> gatk4/createsequencedictionary (#260) ... * fix: update and sort filters * fix: rename gatk/createsequencedictionary -> gatk4/createsequencedictionary	2021-03-08 14:45:46 +01:00
Maxime Garcia	ea6fde0193	Merge pull request #252 from MaxUlysse/master_tiddit ... New module: tiddit	2021-02-25 09:34:33 +01:00
MaxUlysse	f62196a4a6	feat: add tiddit_sv module	2021-02-24 15:59:10 +01:00
JoseEspinosa	e9fc285967	Fix conda version declaration	2021-02-24 15:52:25 +01:00
Harshil Patel	50b98d56a1	Merge pull request #246 from drpatelh/master ... Update iVar modules	2021-02-24 13:00:05 +00:00
drpatelh	1094af2206	Add missing docs	2021-02-24 12:54:45 +00:00
Harshil Patel	ca4b4eb78e	Merge pull request #248 from JoseEspinosa/fix_bcftools ... Add missing requirements to bcftools modules	2021-02-24 12:51:39 +00:00
FriederikeHanssen	4673c119c7	resolve merge conflicts	2021-02-24 10:03:16 +01:00
JoseEspinosa	ec674bb127	Add label to bcftools processes	2021-02-24 09:47:54 +01:00
JoseEspinosa	823a631afc	Fix tools entry on yml	2021-02-24 09:47:36 +01:00
Jose Espinosa-Carrasco	8f4363ccb5	Merge pull request #247 from JoseEspinosa/bcftools-mpileup ... Add bcftools mpileup module	2021-02-24 09:24:43 +01:00
JoseEspinosa	af7bc743bf	Correct yml file, add fasta to input and correct vcf on output	2021-02-24 09:15:18 +01:00
Harshil Patel	5287fe5f95	Merge pull request #245 from phue/bismark_deduplicate ... add bismark/deduplicate + tests	2021-02-23 21:08:24 +00:00
Harshil Patel	4703a60443	Merge pull request #220 from phue/bwameth ... add bwameth modules	2021-02-23 21:01:54 +00:00
JoseEspinosa	138be9f918	Adding label to the bcftools-mpileup process	2021-02-23 21:52:15 +01:00
drpatelh	89cd71309c	Output log file for MultiQC	2021-02-23 20:36:23 +00:00
drpatelh	9098ba41c8	Update ivar consensus	2021-02-23 20:36:03 +00:00
JoseEspinosa	035443b6e0	Add bcftools-mpileup module	2021-02-23 19:05:26 +01:00
phue	e73bda26f5	add bismark/deduplicate + tests	2021-02-23 18:02:16 +01:00
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
kevinmenden	3fee38ee2d	added gatk4 revertsam	2021-02-22 15:21:39 +01:00
kevinmenden	efd60d94ee	adding revertsam/ fix typo in mergevcfs	2021-02-22 15:10:20 +01:00
kevinmenden	69d7bb4fca	reformatted input to tuple	2021-02-22 13:31:54 +01:00
phue	bf0e0d857d	bwameth/align: fix fasta name retrieval ... apparently bwameth doesn't like './' in front of the filepath? I have no idea. This works however	2021-02-20 13:12:43 +01:00
phue	c67e591caf	apply suggestions from review ... thanks @drpatelh	2021-02-20 12:51:01 +01:00
kevinmenden	bb5c0ceca5	adding SplitNCigarReads	2021-02-19 14:59:29 +01:00
Kevin Menden	0202162b17	Merge branch 'master' into gatk4-mergevcfs	2021-02-19 14:11:30 +01:00
kevinmenden	02abe106ec	added optional reference dictionary as input	2021-02-19 14:09:32 +01:00
kevinmenden	c288e081b4	initial commit adding mergevcfs	2021-02-19 13:29:08 +01:00
Kevin Menden	5c325f2942	Merge branch 'master' into master	2021-02-19 13:08:43 +01:00
kevinmenden	bd8ba42a8d	added gatk4 SamToFastq	2021-02-19 12:41:29 +01:00
kevinmenden	6dcaf5ffc8	add gatk4 bedtointervallist	2021-02-19 11:26:31 +01:00
phue	a963c67481	bwameth: pass genome index as directory ... instead of single files	2021-02-18 11:51:36 +01:00
phue	0d8f5f0572	add bismark/genome_preparation + tests	2021-02-18 10:56:36 +01:00
Patrick Hüther	dba295155e	Merge pull request #219 from phue/qualimap_bamqc ... add qualimap/bamqc + test	2021-02-18 10:09:03 +01:00
phue	0606c06a25	qualimap/bamqc: remove unneeded variable definition ... can just use task.cpus directly	2021-02-18 10:00:49 +01:00
Harshil Patel	5695e4ccce	Merge pull request #222 from phue/methyldackel ... add methyldackel modules	2021-02-17 22:17:26 +00:00
Harshil Patel	ecd26b388d	Merge pull request #221 from heuermh/seqwish ... Add module for seqwish/induce	2021-02-17 22:14:49 +00:00
phue	52b00d4286	add methyldackel/mbias + tests	2021-02-17 19:27:57 +01:00
phue	5ad7c6bc51	add methyldackel/extract + tests + testdata	2021-02-17 19:18:55 +01:00
phue	84a5da0d91	add bwameth/align module + tests	2021-02-17 18:23:11 +01:00
Michael L Heuer	206b605666	Add module for seqwish/induce	2021-02-17 11:19:47 -06:00
phue	180b1cf36b	add bwameth/index module + test	2021-02-17 18:03:48 +01:00