1952 commits

This branch

This branch

All branches

Author	SHA1	Message	Date
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
kevinmenden	02abe106ec	added optional reference dictionary as input	2021-02-19 14:09:32 +01:00
MaxUlysse	2bf3890afb	Merge remote-tracking branch 'upstream/master' into master_tiddit	2021-02-19 13:37:45 +01:00
kevinmenden	3ac5c5fad6	working test	2021-02-19 13:36:42 +01:00
Kevin Menden	7996a46178	Merge pull request #235 from KevinMenden/master ... add gatk4 bedtointervallist	2021-02-19 13:35:15 +01:00
kevinmenden	c0693fa3db	remove whitespace	2021-02-19 13:30:40 +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
Kevin Menden	134f0ac78c	Merge pull request #236 from KevinMenden/gatk4-bamtofastq ... added gatk4 SamToFastq	2021-02-19 13:07:10 +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
MaxUlysse	eaff4eb0ff	fix: order alphabetically	2021-02-19 10:56:04 +01:00
Harshil Patel	01c0d335ca	Merge pull request #223 from phue/bismark_genome_preparation ... add bismark/genome_preparation + test	2021-02-18 19:08:00 +00:00
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