✈️ ica pilot #197
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✈️ ica pilot #197
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dmiller15
added
bug
migbro
reviewed
May 1, 2025
| when: $(inputs.input[3] != null) | ||
| when: $(inputs.run_step != null) | ||
| in: | ||
| run_step: supplement_vcfs |
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Ah, ok, kind of doing like a variable assignment for clarity instead of referring to an array position, nice
| } | ||
| if (inputs.flag != "N"){ | ||
| cmd += "bedtools intersect -a " + inputs.input_vcf.path + " -b " + inputs.input_bed_file.path + " -header -wa > " + out_vcf + " && "; | ||
| cmd += "bedtools intersect -a " + (inputs.input_vcf ? inputs.input_vcf.path : "") + " -b " + inputs.input_bed_file.path + " -header -wa > " + out_vcf + " && "; |
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Hmmm, if inputs.input_vcf is null, then give empty string to -a? How does that work?
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This is to get around a "null has no attribute path" error. In reality if the input_vcf is not provided, we'll have exited anyway.
| if (ary != null){ | ||
| for(var i = 0; i < ary.length; i++) { | ||
| if(Array.isArray(ary[i])) { | ||
| ret = ret.concat(flatten(ary[i])); |
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Dangerous if we have infinitely nested lists 🐰
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| } | ||
| } | ||
| return '' |
| source: [strelka2/strelka2_protected_outputs, mutect2/mutect2_protected_outputs, lancet_input_vcf] | ||
| valueFrom: | | ||
| $(self.filter(function(e) { return e != null }).map(function(e) { return e.filter(function(i) { return i.basename.search(/(.vcf|.vcf.gz)$/) != -1 }) }).reduce(function(a,c) { return a.concat(c) })) | ||
| $(self.filter(function(e) { return e != null }).map(function(e) { return e.filter(function(i) { return i.basename.search(/(.vcf|.vcf.gz)$/) != -1 }) }).reduce(function(a,c) { return a.concat(c) }, [])) |
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I always found these one-liner formats to be so difficult to read
wongjessica93
approved these changes
May 1, 2025
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Description
Feel free to ignore the packed workflow in the review. It's just there to expedite workflow updating for ICA.
Made the following changes:
Part of https://d3b.atlassian.net/browse/BIXU-3907
Type of change
Please delete options that are not relevant.
How Has This Been Tested?
Please describe the tests that you ran to verify your changes. Provide instructions so we can reproduce. Please also list any relevant details for your test configuration
Test Configuration:
Checklist: