Added germline CNV WDL workflows - #3071
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samuelklee
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samuelklee
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Just a few minor comments and questions.
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| # Output file name depending on type of coverage | ||
| String cov_output_name = if (is_wgs && (select_first([transform, ""]) == "RAW")) then "${base_filename}.coverage.tsv.raw_cov" else "${base_filename}.coverage.tsv" |
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Can we change the filenames to ${base_filename}.coverage.raw.tsv and ${base_filename}.coverage.pcov.tsv?
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Actually, perhaps @sooheelee can comment if changing ${base_filename}.coverage.tsv to ${base_filename}.coverage.pcov.tsv when transform = "PCOV" will necessitate changes to the javadoc examples for the somatic CNV tools. If so, let's just make the ${base_filename}.coverage.tsv.raw_cov to ${base_filename}.coverage.raw.tsv change for now.
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It appears we populate our WDL scripts repo using this python script: https://github.com/broadinstitute/wdl/blob/develop/scripts/wrappers/gatk/gatkToWdlWrapper.py. At glance, it doesn't appear to require the javadoc portion of code, which is what I remember being the original target. Let's ask @knoblett to confirm.
Since you are providing recommended workflows in WDL scripts within the repo, I think as long as these are up to date, and the documentation is up to date, the WDL repo translation is less of a concern as it lists all of the tool's arguments as task variables.
I think this is what you are asking? Or are you just letting me know of these changes? I can change these in the example commands given in the javadoc portion if needed. It's no problem.
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Just confirmed that the WDL repo's scripts are based on the gatkDoc generated json files, which in turn are parsed from the code portion and not the doc portion.
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Actually, I was just letting you know of the change so you could update the example command. But after discussing with @asmirnov239 we decided to hold off on the pcov change.
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@sooheelee @knoblett I wasn't aware we had internal scripts that read the gatkDoc-generated json files. The GATK4 json is somewhat different than GATK3, and the python script referenced above appears to be dependent on GATK3. @knoblett Is anyone running (or intending to run) that script on GATK4 json ? If so we probably need to make some changes to get it to work.
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@cmnbroad These are scripts that live in the WDL repo. We will want to run them at some point, yes, but it's ok if there's some tweaking needed at that time. We're leaving that for when we're past the beta and close to the general release.
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@vdauwera Ok great - they will definitely need some tweaking.
| "/home/travis/build/broadinstitute/gatk-protected/src/test/resources/large/cnv_germline_workflows_test_files/resources/homo_sapiens_germline_CN_transition_matrix_XY_Y.tsv" ], | ||
| "CNVGermlinePanelWorkflow.num_latents": "2", | ||
| "CNVGermlinePanelWorkflow.targets": "/home/travis/build/broadinstitute/gatk-protected/src/test/resources/large/cnv_germline_workflows_test_files/inputs/ice_targets_chr20xy.tsv", | ||
| "CNVGermlinePanelWorkflow.CollectCoverage.disable_all_read_filters": "false", |
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Why is this set to false only in the panel workflows?
| CROMWELL_JAR="cromwell-0.26.jar" | ||
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| # Panel WES | ||
| java -jar ~/${CROMWELL_JAR} run /home/travis/build/broadinstitute/gatk-protected/scripts/cnv_wdl/germline/gCNV_panel_creation_workflow.wdl gCNV_panel_creation_workflow_wes.json |
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Let's change the filenames of WDL workflows/templates to start with cnv_germline_ rather than gCNV_, to be more analogous to the somatic filenames. But you can keep "gCNV" in tasknames, etc. for now.
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Codecov Report
@@ Coverage Diff @@
## master #3071 +/- ##
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+ Coverage 80.129% 80.133% +0.005%
Complexity 16970 16970
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Files 1143 1143
Lines 61566 61565 -1
Branches 9592 9592
===============================================
+ Hits 49332 49334 +2
+ Misses 8417 8414 -3
Partials 3817 3817
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… added gCNV wdl files, set up travis testing of the gCNV WDL workflows, created gCNV template input files and gCNV resources directory
6 participants
Migration of the broadinstitute/gatk-protected#1076 PR.