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875 commits 30 branches 0 tags 142 MiB
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200 commits

Author SHA1 Message Date
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
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
Edmund Miller
6fe7b48b5b
Revert "Run alllll the testsgit add .github/workflows/pytest-workflow.yml" 
This reverts commit ffc218e51b.
 2021-02-03 20:08:11 -06:00
Edmund Miller
431c699727
Revert "ci: Test bowtie-build instead of _" 
This reverts commit 9b454416d2.
 2021-02-03 20:06:05 -06:00
drpatelh
ffc218e51b
Run alllll the testsgit add .github/workflows/pytest-workflow.yml 2021-02-03 20:03:45 -06:00
drpatelh
0c88ff7458
Upgrade Singularity and change TMPDIR for pytest output 2021-02-03 20:03:43 -06:00
Edmund Miller
9b454416d2
ci: Test bowtie-build instead of _ 2021-02-03 13:17:14 -06:00
Edmund Miller
7dbac4bdef
ci: Test adding another work to test name 2021-02-03 13:17:14 -06:00
Edmund Miller
b058da5856
ci: Test buil to see if build is special 2021-02-03 12:43:18 -06:00
Edmund Miller
6901c7e830
ci: Fix bowtie_build names with "" 2021-02-03 12:37:14 -06:00
drpatelh
ff6f0642d2 Fix multiqc tests 2021-02-03 17:43:14 +00:00
drpatelh
38c3ecfac6 Merge branch 'master' of https://github.com/nf-core/modules into split_tests 2021-02-03 16:05:06 +00:00
drpatelh
743ba37d4b Update filters paths 2021-02-03 16:04:43 +00:00
drpatelh
3968c18fd7 Only run Docker tests 2021-02-03 14:04:58 +00:00
drpatelh
9e44b0f4f2 Add conda clean step to action 2021-02-03 12:57:55 +00:00
drpatelh
49fecaa4f0 Switch channel order 2021-02-03 12:07:39 +00:00
drpatelh
d783e2d535 Only test Docker and Conda 2021-02-03 09:02:12 +00:00
Edmund Miller
54bb0ae7a1
ci: Name logs 2021-02-02 17:51:20 -06:00
Edmund Miller
42b8962320
ci: Add bioconda channels 2021-02-02 17:13:35 -06:00
Edmund Miller
0813e61c01
ci: Kick off all container types 2021-02-02 17:08:10 -06:00
Edmund Miller
725de25ce4
Revert "ci: Only test docker for now" 
This reverts commit c63ba06777.
 2021-02-02 17:03:29 -06:00
Edmund Miller
c63ba06777
ci: Only test docker for now 
I can't access the artifacts.
 2021-02-02 16:49:03 -06:00
Edmund Miller
bb3196ddeb
ci: Update name to use matrix 2021-02-02 16:49:03 -06:00
Edmund Miller
dcfd1089e5
ci: Add --keep-workflow-wd-on-fail 2021-02-02 16:49:03 -06:00
Edmund Miller
983b024010
ci: Use ubuntu-20.04 for singularity 2021-02-02 16:49:02 -06:00
Edmund Miller
8cd6e41df9
ci: Change singularity version 3.6.4 => 3.5.3 
Per @grst having issues after 3.6
 2021-02-02 16:49:02 -06:00
Edmund Miller
bf2e027fdf
ci: Remove conda to kickoff CI 2021-02-02 16:48:58 -06:00
Edmund Miller
1e9aad430d
ci: Remove ${{}} for style points 
It's not necessary in if statements
 2021-02-02 15:40:30 -06:00
Edmund Miller
654c6225f0
ci: Setup multiple profiles for testing 
Added conda and singularity
 2021-02-02 15:38:51 -06:00
Edmund Miller
35ac5c5f15
ci: Add filters for new modules 
These snuck in after the 506ebe5 was written
 2021-02-02 15:27:45 -06:00
Edmund Miller
341fa43ae3
ci: Add PROFILE ahead of pytest run 2021-02-02 13:07:58 -06:00
Harshil Patel
e7b1241449
Merge pull request #120 from nf-core/composite-runs 
Universal CI job
 2021-02-02 18:26:02 +00:00
Edmund Miller
ce2a5b32f5
refactor: Move away from composite-action 2021-02-02 12:21:36 -06:00
drpatelh
f84e5b59ca Rename bowtie_index to bowtie_build 2021-02-01 17:53:31 +00:00
Harshil Patel
0a41130276
Merge pull request #131 from KevinMenden/fastp-module 
Adding fastp module
 2021-02-01 13:43:35 +00:00
Harshil Patel
e851da8640
Merge pull request #130 from KevinMenden/master 
Adding a QUAST module
 2021-02-01 13:17:57 +00:00