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Author SHA1 Message Date
Harshil Patel
85926b20d4
Merge pull request #134 from JoseEspinosa/bcftools_viralrecon 
Bcftools viralrecon
 2021-02-08 21:52:57 +00:00
Harshil Patel
13c1e908a3
Update .github/filters.yml 2021-02-08 21:48:21 +00:00
Harshil Patel
0f6830f7cc
Update tests/software/bcftools/consensus/main.nf 2021-02-08 21:41:24 +00:00
JoseEspinosa
58d28ed896 Fix copy/paste error :P 2021-02-08 21:57:31 +01:00
JoseEspinosa
f8882de456 Renaming test ymls just to: software tool 2021-02-08 21:56:53 +01:00
JoseEspinosa
7a0ba85843 Adding again bcftools modules to filters after solving conflict 2021-02-08 18:10:50 +01:00
JoseEspinosa
f4e322f88d Merging upstream changes 
# Conflicts:
#	.github/filters.yml
 2021-02-08 18:09:41 +01:00
JoseEspinosa
4fa38ebb7a Separate test data to break dependencies between bcftools modules tests 2021-02-08 16:51:21 +01:00
JoseEspinosa
83cc25860d Rearranging tests to test each module separately 2021-02-08 15:16:51 +01:00
JoseEspinosa
fe412797dd Adressing general comments on PR #134 2021-02-08 15:11:36 +01:00
Harshil Patel
d29ef5c52c
Merge pull request #152 from drpatelh/docs 
Update template module and add more docs for testing and finding containers
 2021-02-08 10:31:00 +00:00
JoseEspinosa
5071bf5914 Merge remote-tracking branch 'upstream/master' into bcftools_viralrecon 2021-02-08 10:45:57 +01:00
drpatelh
c9cfdd31f3 Fix barfing linters 2021-02-08 00:57:06 +00:00
drpatelh
c92fe8701a Add docs about docs 2021-02-08 00:53:32 +00:00
drpatelh
41dfaf2a19 Use Nextflow comments 2021-02-08 00:44:45 +00:00
drpatelh
56752b90f5 Fix indents 2021-02-08 00:40:36 +00:00
drpatelh
a8efd112b9 Add docs about finding and adding containers 2021-02-08 00:35:50 +00:00
drpatelh
d4b278eb65 Update docs 2021-02-08 00:01:48 +00:00
drpatelh
9cb958ca25 Update commands for pytest 2021-02-07 23:50:21 +00:00
drpatelh
07f62a76c5 Re-word CI tests 2021-02-07 23:40:26 +00:00
drpatelh
6bbb71a022 Update link to tests template 2021-02-07 23:26:54 +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
Harshil Patel
dcabde6b85
Merge pull request #139 from nf-core/testing-docs 
Add documentation for Testing
 2021-02-07 22:35:01 +00:00
Harshil Patel
e4adb8ab53
Merge pull request #79 from Functional-Genomics-Lab/bedtools-general 
Bring bedtools up to speed
 2021-02-07 20:49:17 +00:00
Harshil Patel
0393d39105
Update tests/software/bedtools/complement/main.nf 2021-02-07 20:35:51 +00:00
Harshil Patel
5269c1ec60
Update tests/software/bedtools/intersect/main.nf 2021-02-07 20:35:12 +00:00
Harshil Patel
8841af1267
Update tests/software/bedtools/merge/main.nf 2021-02-07 20:34:30 +00:00
Harshil Patel
b068f2fc53
Update tests/software/bedtools/sort/main.nf 2021-02-07 20:33:02 +00:00
Harshil Patel
b260192942
Merge pull request #149 from heuermh/minimap2 
Add minimap2 align module
 2021-02-07 16:37:26 +00:00
Michael L Heuer
35ed09b06e Fix CI test failure 2021-02-05 11:41:36 -06:00
Michael L Heuer
6b873d7d33 Remove single_end if/else 2021-02-05 11:35:11 -06:00
Edmund Miller
e51d0bdf5e
Apply suggestions from code review 
Co-authored-by: Kevin Menden <kevin.menden@t-online.de>
 2021-02-05 09:26:45 -06:00
Harshil Patel
31520fce97
Update software/minimap2/align/main.nf 2021-02-05 10:45:34 +00:00
Kevin Menden
17dd0415f2
Merge pull request #146 from heuermh/bandage 
Add bandage image module
 2021-02-05 08:00:44 +01:00
Edmund Miller
f065476d36
docs: Add testing documentation 2021-02-04 16:00:31 -06:00
Michael L Heuer
50bebac136 Remove pairwise test 2021-02-04 15:22:12 -06:00
Michael L Heuer
061b13bf25 Fix md5 --> md5sum 2021-02-04 13:48:56 -06:00
Michael L Heuer
bbc8c725a2 Fix lint errors 2021-02-04 13:45:39 -06:00
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
Kevin Menden
089af956fb
Merge pull request #148 from nf-core/fix-artifact-path 
ci: Fix artifact path
 2021-02-04 15:48:52 +01:00
Edmund Miller
05c09429a3
ci: Fix artifact path 
Had to change it for singularity
 2021-02-04 08:45:34 -06:00
Harshil Patel
08d8443510
Merge pull request #143 from nf-core/ci-fixes 
Get Singularity CI tests working
 2021-02-04 11:28:49 +00:00
Harshil Patel
5aa920eb53
Update tests/software/bowtie/align/test.yml 2021-02-04 10:19:28 +00:00
Harshil Patel
68f9a0b711
Update tests/software/bowtie/build/test.yml 2021-02-04 10:08:01 +00:00
Harshil Patel
eb45368a35
Update tests/software/bowtie2/build/test.yml 2021-02-04 10:07:44 +00:00
Kevin Menden
f298c594fe
Update meta.yml 
Just a small edit, we want to keep this consistent for linting
 2021-02-04 07:34:08 +01:00
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