366 commits

Author	SHA1	Message	Date
JoseEspinosa	155c2a1185	Check only for vcf file to exists (includes cmd)	2021-02-26 07:14:29 +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
Harshil Patel	50b98d56a1	Merge pull request #246 from drpatelh/master ... Update iVar modules	2021-02-24 13:00:05 +00:00
FriederikeHanssen	4673c119c7	resolve merge conflicts	2021-02-24 10:03:16 +01:00
FriederikeHanssen	7627e656ee	Add all tests back in	2021-02-24 09:57:23 +01:00
FriederikeHanssen	8a7333c13b	lower case path	2021-02-24 09:53:11 +01:00
FriederikeHanssen	7f6e5d9ab5	try to make a single test pass on GHA, passes locally	2021-02-24 09:48:55 +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
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
drpatelh	b581bdc36c	Update test script	2021-02-23 20:43:05 +00:00
drpatelh	aaaef7df8c	Add BAM index	2021-02-23 20:42:16 +00:00
JoseEspinosa	e9d90007c5	Adding arguments to make md5 hashes stable	2021-02-23 19:39:24 +01:00
JoseEspinosa	4b3c86ed9f	Add tests for bcftools-mpileup	2021-02-23 19:05:57 +01:00
phue	e73bda26f5	add bismark/deduplicate + tests	2021-02-23 18:02:16 +01:00
FriederikeHanssen	e67515809a	try to only make paired-end test work, pass locally with conda & docker	2021-02-23 15:47:16 +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	312bf85f70	use reasonable option params	2021-02-23 11:26:54 +01:00
FriederikeHanssen	9c51e05125	remove wrong md5 sums	2021-02-23 11:25:45 +01:00
FriederikeHanssen	c7d2bc8d43	Add tests for different options	2021-02-23 11:14:51 +01:00
FriederikeHanssen	ec63f335d5	Add split2 options	2021-02-22 22:43:32 +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
kevinmenden	43446bc37e	added sarscov2 fastq and bam files	2021-02-22 13:19:12 +01:00
phue	2d8baa8b75	bwameth/index: update test.yml	2021-02-20 12:55:09 +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	3ac5c5fad6	working test	2021-02-19 13:36:42 +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	908e55ee5c	fixed tag	2021-02-19 12:46:59 +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
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	1a414261c4	bwameth/align: update checksums	2021-02-17 18:35:39 +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