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| primaryDescriptorPath: /PECGS-QUICviz/QUICviz.wdl | ||
| testParameterFiles: | ||
| - /PECGS-QUICviz/QUICviz.inputs.json | ||
| - name: CoverageProfiler |
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Can you add a CoverageProfiler.md describing what the pipeline does?
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I will add a README.md page.
| cpu: select_first([cpu, 1]) | ||
| docker: samtools_docker | ||
| disks: "local-disk ~{disk_size_gb} SSD" | ||
| preemptible: 0 |
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preemptible should be a variable, and probably should default to 1. Is there a reason you are choosing 0 as the default?
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For testing. I will make it a variable.
| "coverageProfile.MinBaseQuality": "Int (optional, default = 20)", | ||
| "coverageProfile.cnv_depth_profile": "Boolean (optional, default = false)", | ||
| "coverageProfile.CovProfileViz.CovProfileViz_docker": "String (optional, default = \"us-central1-docker.pkg.dev/tag-team-160914/gptag-dockers/covprofileviz:0.0.0\")", | ||
| "coverageProfile.CovProfileViz.preemptible": "Int? (optional, default = 3)", |
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I know it is common to use a default of 3, but I think it is usually best to do a default of 1.
Where is this default getting enforced? Is this enforced by the WDL?
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It is enforced by the WDL.
| Int MinMappingQuality = 20 | ||
| Boolean visualise_coverage = false | ||
| } | ||
| if (coverageTool =="Samtools") { |
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We should consider adding a linter so that we can fix things like whitespace without going through a review.
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Interesting. I am surprised Winstanley WDL didn't suggest that change. There is a WDL lint we could incorporate. But, it is not as convenient as a IDE plugin.
https://github.com/dnanexus/wdlTools/blob/develop/doc/Commands/Lint.md
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This is a WDL that I created to get depth profile for TAG#1956. Currently, it can supports getting depth profile from Samtools depth and GATK DepthOfCoverage. The visualization script supports WES data.