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Vector CNV pipeline version 1.0.0 #116

Merged
merged 133 commits into from
Jan 10, 2024
Merged

Vector CNV pipeline version 1.0.0 #116

merged 133 commits into from
Jan 10, 2024

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jessicaway
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@kevinpalis
Initial commit for the CNV container.
2697dda
@kevinpalis
Adding utility sript to easily build this image and push to Broad's GCR.
871033c
@kevinpalis
First attempt at CNV WDL.
56a833f
@kevinpalis
Added dockstore entry.
4ef3848
@kevinpalis
Test commit
0011a1b
@kevinpalis
Trying to get a hello-world wdl to work so I can import this to Terra…
4c98eb5 
… from Dockstore.
@kevinpalis
Fixing wrong imports
1a7872c
@kevinpalis
Trying to get this to work in Dockstore first.
f8090b8
@kevinpalis
Testing variable assignments in Terra.
21eda95
@kevinpalis
Testing out the new container in terra.
15c06ae
@kevinpalis
Fixes to dockerbuild for CNV. Adding new draft WDL to CNV.
4ec8bbf
@kevinpalis
Fixes to dockerbuild for CNV. Adding new draft WDL to CNV.
483dd78
@kevinpalis
Debugging to determine actual dir struct on Terra
7d98489
@kevinpalis
Debugging to determine actual dir struct on Terra
fbc487d
@kevinpalis
Adding required parameters to the pipeline.
95e47da
@kevinpalis
New docker built.
6d8ceca
@kevinpalis
Merge pull request #113 from malariagen/master
5d1ec66 
Updating feature branch with the latest master branch.
@kevinpalis
Using new container with updated script.
992e352
@kevinpalis
Moving away from calling shell scripts, calling python directly form WDL
8f85cc5
@kevinpalis
Removing disk declaration as Terra wasn't happy about it.
2e8b9b9
@kevinpalis
Changing ram value
4f1c40f
@kevinpalis
Fixing a mistyped variable
f0ab218
@kevinpalis
Absolute path for output doesn't seem to work in Terra
724b7be
@kevinpalis
Fixing localization issues.
78c74a8
@kevinpalis
Debugging. File handling in terra is a pain.
313fdd1
@kevinpalis
Trying out compressing the output directory
e1eca6d
@kevinpalis
Weird WDL error on mixed whitespaces
5ebcc7d
@kevinpalis
Weird WDL error on mixed whitespaces
1f81676
@kevinpalis
Fixing directory paths. Adding missing coveragelogs dir.
a3908be
@kevinpalis
Parameterizing window size
be89ec6
nikellepetrillo
nikellepetrillo approved these changes Jan 10, 2024
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looks good! just a few small suggestions

@jessicaway jessicaway merged commit 3152d9e into master Jan 10, 2024
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@jessicaway jessicaway deleted the jw_add_target_regions_subpipeline branch January 10, 2024 21:09
@jessicaway jessicaway restored the jw_add_target_regions_subpipeline branch January 10, 2024 21:09
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@nikellepetrillo nikellepetrillo nikellepetrillo approved these changes

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3 participants
@jessicaway @nikellepetrillo @kevinpalis