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1071 commits 30 branches 0 tags 142 MiB
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234 commits

Author SHA1 Message Date
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
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
7f35a1742d chores: add gatk/createsequencedictionary module 2021-02-16 13:40:06 +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
JoseEspinosa
1e9b88b33c Fixing trailing slashes in .github/filters.yml 2021-02-09 18:16:16 +01:00
JoseEspinosa
e118bc049a Add bedtools getfasta module 2021-02-09 17:56:51 +01:00
JoseEspinosa
9a11e90892 Fixing tests 2021-02-09 17:07:23 +01:00
JoseEspinosa
12ae7b0bff Adding blast blastn module 2021-02-09 16:58:36 +01:00
JoseEspinosa
d0f09e26b6 Adding blast makeblastdb module to filters.yml 2021-02-09 15:47:53 +01:00
JoseEspinosa
c93e96101a Add untar module 2021-02-09 11:50:32 +01:00
JoseEspinosa
f7f06dd6e8 Add gunzip module 2021-02-09 10:05:55 +01:00
Harshil Patel
46e5df2cf7
Merge pull request #151 from drpatelh/bedtools 
Follow up fixes for bedtools modules added in #79
 2021-02-09 01:54:31 +00:00
Harshil Patel
84cf5ea2ef
Merge pull request #153 from JoseEspinosa/bedtools_maskfasta 
Add bedtools maskfasta module
 2021-02-08 23:11:00 +00:00
JoseEspinosa
02d10c25a3 Add bedtools maskfasta module 2021-02-08 23:41:10 +01:00
Harshil Patel
13c1e908a3
Update .github/filters.yml 2021-02-08 21:48:21 +00:00
JoseEspinosa
58d28ed896 Fix copy/paste error :P 2021-02-08 21:57:31 +01:00
JoseEspinosa
7a0ba85843 Adding again bcftools modules to filters after solving conflict 2021-02-08 18:10:50 +01:00
drpatelh
c9cfdd31f3 Fix barfing linters 2021-02-08 00:57:06 +00:00
drpatelh
eeb496cf5c Fix filters 2021-02-07 23:23:08 +00:00
drpatelh
83a50d8ae0 Rename SOFTWARE_TOOL to TOOL_SUBTOOL 2021-02-07 23:20:53 +00:00
drpatelh
418bd64e80 Test module with Conda 2021-02-07 21:33:42 +00:00
sruthipsuresh
93e414635b Fixed md5sum, fixed filters, fixed slop input 2021-01-29 23:17:44 -06:00
sruthipsuresh
ac7f634675 Added complement test 2021-01-29 23:17:44 -06:00
sruthipsuresh
84b66e4f38 Fixed testing, rebased 2021-01-29 23:17:44 -06:00
sruthipsuresh
70de0331a5 Corrected pytest and config 2021-01-29 23:17:44 -06:00
sruthipsuresh
32564137fd Corrected workflows and ran editor config 2021-01-29 23:17:44 -06:00
sruthipsuresh
672f94f2af rebased and updated all bedtools testing and modules 2021-01-29 23:17:44 -06:00
Harshil Patel
b260192942
Merge pull request #149 from heuermh/minimap2 
Add minimap2 align module
 2021-02-07 16:37:26 +00:00
Kevin Menden
17dd0415f2
Merge pull request #146 from heuermh/bandage 
Add bandage image module
 2021-02-05 08:00:44 +01:00
Michael L Heuer
d5f2f5e32d Add minimap2 align module 2021-02-04 13:42:08 -06:00
Michael L Heuer
37a9f6f456 Address review comments 2021-02-04 12:10:54 -06:00
Edmund Miller
05c09429a3
ci: Fix artifact path 
Had to change it for singularity
 2021-02-04 08:45:34 -06:00
Edmund Miller
d48e865401
ci: Use bowtie filter 
This will cause a bit of duplication, but it appears to work. Still the
same logic, because any changes to bowtie*/build will run the align
modules also. So the bowtie_align tags may not even be necessary, since
we can't seem to get the bowtie*_build tags to kick off on their own
anyways. Thank you for coming to my TED talk.
 2021-02-03 20:15:56 -06:00