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Author SHA1 Message Date
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
kevinmenden
02abe106ec added optional reference dictionary as input 2021-02-19 14:09:32 +01:00