omit --dirs from the MultiQC invocation to only show sample names in report #467
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…report omit --dirs from the MultiQC invocation to only show sample names in report; and provide a boolean to optionally enable display of full paths
pipes/WDL/tasks/tasks_reports.wdl
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| @@ -464,6 +464,7 @@ task MultiQC { | |||
| Array[String]? module_to_use | |||
| Boolean data_dir = false | |||
| Boolean no_data_dir = false | |||
| Boolean show_sample_names_with_paths = false | |||
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Is there a reason why we’d actually want to support the —dirs argument in WDL? We could probably drop this parameter
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Theoretically to disambiguate same-name samples
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If the "sample name" (without the --dirs argument) is simply the basename of the filename, I think we already did some work earlier to ensure that our demux task was emitting unique filenames for everything (e.g. appending lane numbers and such to the filename so that our nextseq output files were all uniquely named)
| @@ -447,7 +447,7 @@ task aggregate_metagenomics_reports { | |||
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| task MultiQC { | |||
| input { | |||
| Array[File] input_files = [] | |||
| Array[File] input_files | |||
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I think the original thinking for this default empty assignment was so execution engines like Terra and dnanexus wouldn’t bother the user by default to fill it in if they wanted to omit it. That said… I can’t think off the top of my head where we’d currently have the multiqc task called in a workflow with inbound inputs so maybe this was pointless
MultiQC task: Remove param to toggle path prefixes in sample names
omit
--dirsfrom the MultiQC invocation to only show sample names in report; and provide a boolean to optionally enable display of full pathsAddresses #466