Code

Vector CNV pipeline version 1.0.0#116

Code

Merged

jessicaway merged 133 commits intomastermalariagen/pipelines:masterfrom jw_add_target_regions_subpipelinemalariagen/pipelines:jw_add_target_regions_subpipelineCopy head branch name to clipboardJan 10, 2024

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Commits

Commits on Feb 22, 2023

• Initial commit for the CNV container.

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Commits on Feb 27, 2023

• Adding utility sript to easily build this image and push to Broad's GCR.

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Commits on Mar 1, 2023

• First attempt at CNV WDL.

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• Added dockstore entry.

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• Test commit

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Commits on Mar 3, 2023

• Trying to get a hello-world wdl to work so I can import this to Terra from Dockstore.

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• Fixing wrong imports

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• Trying to get this to work in Dockstore first.

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Commits on Mar 7, 2023

• Testing variable assignments in Terra.

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• Testing out the new container in terra.

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Commits on Mar 20, 2023

• Fixes to dockerbuild for CNV. Adding new draft WDL to CNV.

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• Fixes to dockerbuild for CNV. Adding new draft WDL to CNV.

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Commits on Mar 21, 2023

• Debugging to determine actual dir struct on Terra

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• Debugging to determine actual dir struct on Terra

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• Adding required parameters to the pipeline.

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Commits on Mar 22, 2023

• New docker built.

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• Merge pull request #113 from malariagen/master

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• Using new container with updated script.

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Commits on Mar 23, 2023

• Moving away from calling shell scripts, calling python directly form WDL

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• Removing disk declaration as Terra wasn't happy about it.

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• Changing ram value

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• Fixing a mistyped variable

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• Absolute path for output doesn't seem to work in Terra

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Commits on Mar 24, 2023

• Fixing localization issues.

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• Debugging. File handling in terra is a pain.

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• Trying out compressing the output directory

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Commits on Mar 25, 2023

• Weird WDL error on mixed whitespaces

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• Weird WDL error on mixed whitespaces

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Commits on Mar 27, 2023

• Fixing directory paths. Adding missing coveragelogs dir.

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Commits on Mar 28, 2023

• Parameterizing window size

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• Setting default values for window size and quality min

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Commits on Apr 4, 2023

• Started adding files sent by Eric as parameters to coverage summary task

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• Adding some documentation on params

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• Added all parameters needed by coverage stats

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• Fixing misnamed param meta

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• Removing commented out code that apparently was still causing errors because it is inside an expression bracket

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Commits on Apr 5, 2023

• Adding coverage script execution to command block

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Commits on Apr 10, 2023

• Commenting out CoverageHMM task so I can test the previous steps in Terra

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• Forgot a runtime block

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Commits on Apr 11, 2023

• Catching the log file so it doesn't disappear

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• Adding bai

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Commits on Apr 12, 2023

• Fixed a typo in calling a sample name variable that caused the coveragestats not to find the files

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• Debugging prints because I can't figure out why sample names aren't being picked up in Terra

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Commits on Apr 13, 2023

• Fixing the fix. Dollar sign vs tilde for bash vs WDL variable got me.

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Commits on Apr 14, 2023

• Additional changes

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• Merge branch 'kp_create_cnv_container_PD-2152' into jw_add_target_regions_subpipeline

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Commits on Apr 18, 2023

• Moving on to HMM task while waiting on new BAM files

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Commits on May 2, 2023

• Additional changes

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• Merge branch 'kp_create_cnv_container_PD-2152' into jw_add_target_regions_subpipeline

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Commits on May 12, 2023

• Setting output of coverage summary

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• Setting output of coverage summary

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Commits on May 16, 2023

• Trying out a different approach to dynamic output naming.

  kevinpalis

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• Can't have spaces around the equal sign apparently.

  kevinpalis

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• Doubled the double quotes.

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• Using WDL string sub

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• Fixing error in substitution with floats

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• Replacing with nothing instead of underscore

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• trying to fix missing numbers

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• trying to fix missing numbers

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• trying to fix missing numbers

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• trying to fix missing numbers

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• trying to fix missing numbers

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• trying to fix missing numbers

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• Additional changes

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• Merge branch 'kp_create_cnv_container_PD-2152' into jw_add_target_regions_subpipeline

  jessicaway

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• trying to fix missing numbers

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Commits on May 17, 2023

• Additional changes

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Commits on May 22, 2023

• Adding Terra parameters and proper call to the HMM step.

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• Fixing path as terra finds output relative to cromwell_root

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• Forgot them special variable resolution syntax

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Commits on May 25, 2023

• Fixing missing directory issue.

  kevinpalis

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Commits on May 26, 2023

• Fixing missing directory issue.

  kevinpalis

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• Fixing missing directory issue.

  kevinpalis

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• Cleaning up the code a bit

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Commits on Jun 1, 2023

• Enabling parallel runs again

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Commits on Jun 5, 2023

• Additional changes

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• Merge branch 'kp_create_cnv_container_PD-2152' into jw_add_target_regions_subpipeline

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• Additional changes

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Commits on Jun 6, 2023

• Additional changes

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• Additional changes

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• Additional changes

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Commits on Jun 7, 2023

• Additional changes

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Commits on Jun 9, 2023

• Just a little code cleanup.

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Commits on Jun 12, 2023

• update docker

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• additional changes

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Commits on Jun 14, 2023

• Additional changes

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• where is the Rscripts folder?

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• additional changes

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Commits on Jun 15, 2023

• additional changes

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• add debugging statements

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Commits on Jul 31, 2023

• update scripts with new versions

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Commits on Aug 7, 2023

• updates

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Commits on Aug 14, 2023

• Adding consolidation step for all the tarballs

  kevinpalis

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• Weird WDL to bash syntax conflict resolved

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Commits on Aug 15, 2023

• Plugging in the call to consolidate the tarballs

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Commits on Aug 16, 2023

• Some files are unfortunately lost. Trying if tar can keep them

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• Some files are unfortunately lost. Trying if tar can keep them

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• Current method worked well, no need to manually move files.

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Commits on Aug 18, 2023

• updates

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• Merge branch 'kp_create_cnv_container_PD-2152' into jw_add_target_regions_subpipeline

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• update docker

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Commits on Sep 6, 2023

• remove echos

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• remove Rdata output

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• remove Rdata output

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Commits on Sep 20, 2023

• stop piping output to a log that we don't capture

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Commits on Oct 4, 2023

• explicitly add the coverage dir and diagnostic reads dir

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• fix things

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• fix things again

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• add outputs

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• improvements

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Commits on Nov 3, 2023

• Add CNV coverage calls step to CNV pipeline

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Commits on Nov 14, 2023

• Validates now

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Commits on Nov 15, 2023

• remove unused input

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Commits on Nov 29, 2023

• Update docker

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• Add debugging statement

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• fix bash errors

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Commits on Nov 30, 2023

• Hopefully this lets it run

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• debugging statements

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• this should help

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• this should help

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Commits on Dec 19, 2023

• dynamically set resources for coverage calls step

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• error

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Commits on Jan 9, 2024

• fix dependency graph?

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• fix dependency graph?

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• fix dependency graph?

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• Cleanup

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Commits on Jan 10, 2024

• Update pipelines/copy-number-variation-vector/gcp/CNV.wdl

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• Update pipelines/copy-number-variation-vector/gcp/CNVCoverageCalls.wdl

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• Update pipelines/copy-number-variation-vector/gcp/CNVCoverageCalls.wdl

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• Update pipelines/copy-number-variation-vector/gcp/CNVCoverageCalls.wdl

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• Cleanup

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• Merge remote-tracking branch 'origin/jw_add_target_regions_subpipeline' into jw_add_target_regions_subpipeline

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• Update pipelines/copy-number-variation-vector/gcp/TargetRegions.wdl

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