3321 commits

This branch

This branch

All branches

Author	SHA1	Message	Date
FriederikeHanssen	48d6d88104	Update .github/filters.yml ... Co-authored-by: Kevin Menden <kevin.menden@live.com>	2021-02-24 10:29:13 +01:00
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
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	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
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	e9d90007c5	Adding arguments to make md5 hashes stable	2021-02-23 19:39:24 +01:00
JoseEspinosa	20bcb00ea0	Fix indentation	2021-02-23 19:08:56 +01:00
JoseEspinosa	4b3c86ed9f	Add tests for bcftools-mpileup	2021-02-23 19:05:57 +01:00
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	e67515809a	try to only make paired-end test work, pass locally with conda & docker	2021-02-23 15:47:16 +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
Gregor Sturm	f4af709634	Merge pull request #244 from grst/fix-conda ... Only use one thread for pytest-workflow	2021-02-23 14:15:05 +01:00
Gregor Sturm	38349417ad	Update .github/workflows/pytest-workflow.yml ... Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>	2021-02-23 14:14:29 +01:00
FriederikeHanssen	5e365d5eff	Make all these tests pass	2021-02-23 14:09:46 +01:00
Gregor Sturm	94bdc62123	Only use one thread for pytest-workflow ... This avoids a race condition on the conda cache.	2021-02-23 14:06:52 +01:00
FriederikeHanssen	25a2a16f2d	Try to make a single test pass	2021-02-23 13:34:50 +01:00
FriederikeHanssen	a0c9777d60	add seqkit to GHA	2021-02-23 12:43:30 +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
Kevin Menden	0e594eadc3	Merge pull request #240 from KevinMenden/revertsam ... Added GATK4 Revertsam	2021-02-23 08:25:36 +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
Kevin Menden	5fb90932f7	Merge pull request #238 from KevinMenden/splitcigar ... Splitcigar	2021-02-22 13:59:38 +01:00
kevinmenden	bd585265ce	added entry to filters.yml	2021-02-22 13:36:49 +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
Kevin Menden	c606ea42e7	Merge pull request #237 from KevinMenden/gatk4-mergevcfs ... Gatk4 mergevcfs	2021-02-22 12:53:57 +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	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