Commit graph

263 commits

Author SHA1 Message Date
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
phue
e73bda26f5 add bismark/deduplicate + tests 2021-02-23 18:02:16 +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
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
kevinmenden
3fee38ee2d added gatk4 revertsam 2021-02-22 15:21:39 +01:00
kevinmenden
bd585265ce added entry to filters.yml 2021-02-22 13:36:49 +01:00
Kevin Menden
0202162b17
Merge branch 'master' into gatk4-mergevcfs 2021-02-19 14:11:30 +01:00
kevinmenden
3ac5c5fad6 working test 2021-02-19 13:36:42 +01:00
kevinmenden
c0693fa3db remove whitespace 2021-02-19 13:30:40 +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
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
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
phue
b5b259a2d9 add qualimap/bamqc + test 2021-02-17 17:34:51 +01:00
phue
a156bdfc03 faidx: add filter 2021-02-17 17:01:22 +01:00
Maxime Garcia
842173be9f
Merge pull request #175 from MaxUlysse/master_ISSUE_TEMPLATE
fix: add guidelines to PRs and issues
2021-02-17 00:36:35 +01:00
MaxUlysse
ebb6d5de1f fix: Apply suggestions from code review 2021-02-17 00:34:55 +01:00
Harshil Patel
412172cda6
Merge pull request #180 from MaxUlysse/master_tabix_bgzip
Replace bcftools/bgzip by tabix/bgzip
2021-02-16 23:32:23 +00:00
Maxime Garcia
75d1483417
Apply suggestions from code review
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-02-17 00:32:06 +01:00
Harshil Patel
a282ecd8c7
Merge pull request #172 from andersgs/ivar-variant
Add ivar variants
2021-02-16 23:20:30 +00:00
Harshil Patel
b07ad23efa
Merge pull request #179 from MaxUlysse/master_htslib_tabix
Replace bcftools/tabix by tabix/tabix
2021-02-16 22:30:45 +00:00
Harshil Patel
759079796a
Update .github/filters.yml 2021-02-16 22:24:49 +00:00
MaxUlysse
6a147b8aaa chores: replace bcftools/bgzip by tabix/bgzip cf #179 2021-02-16 19:11:36 +01:00
MaxUlysse
3805eb2dd1 fix: remove bcftools/tabix from filters.yml 2021-02-16 18:38:20 +01:00
MaxUlysse
10524e3515 chores: add modules for htslib/tabix 2021-02-16 14:47:53 +01:00
MaxUlysse
bbee0efd75 fix: add suggestions from reviews 2021-02-16 13:59:21 +01:00
MaxUlysse
7f35a1742d chores: add gatk/createsequencedictionary module 2021-02-16 13:40:06 +01:00
MaxUlysse
a285bfe8a6 fix: add guidelines to PRs and issues 2021-02-16 11:07:43 +01:00
Anders Goncalves da Silva
89f65e0875 Merge branch 'master' into ivar-variant 2021-02-15 20:50:35 -08:00
Harshil Patel
8eb3acc43f
Merge pull request #171 from JoseEspinosa/mosdepth
Add mosdepth module
2021-02-15 23:13:01 +00:00
Anders Goncalves da Silva
4ab3ccc905
Add ivar variants 2021-02-15 09:28:10 -08:00
JoseEspinosa
6e92a6a080 Adding mosdepth module 2021-02-15 14:33:44 +01:00
Maxime Garcia
ec0bf0145e
Merge branch 'master' into master_bwa-mem2 2021-02-15 13:08:52 +01:00
Anders Goncalves da Silva
6dca7799e6
Add ivar trim 2021-02-12 16:02:10 -08:00
Harshil Patel
63a20e7b5c
Merge pull request #168 from JoseEspinosa/bcftools_merge
Add bcftools merge module
2021-02-12 23:20:30 +00:00
JoseEspinosa
5313698705 Add bcftools merge module 2021-02-13 00:08:57 +01:00
Anders Goncalves da Silva
24b212318b Merge branch 'master' into ivar-consensus 2021-02-12 11:51:24 -08:00
Anders Goncalves da Silva
e5a3e3a5b8
Add ivar consensus to filter.yml 2021-02-12 10:59:46 -08:00
JoseEspinosa
6e8b63fc26 Add cat fastq module 2021-02-12 17:22:07 +01:00
MaxUlysse
2f18750964 chores: update filters.yml 2021-02-12 13:53:49 +01:00
JoseEspinosa
68b85d9191 Merge remote-tracking branch 'upstream/master' into bedtools_getfasta 2021-02-09 18:23:24 +01:00