Add FastQC to Optimus and SmartSeq2 #202
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retest this please |
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| File barcoded_bam = select_first([AttachBarcodes.bam_output, AttachBarcodesNoIndex.bam_output]) | ||
| Array[File] fastqc_output_htmls = select_first([FastQC.fastqc_htmls,FastQCNoIndex.fastqc_htmls]) |
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If you are expecting multiple zips or htmls then I think select_all() would be better here.
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Since only one of FastQC and FastQCNoIndex will ever be run, using select_all() would just result in an extra unnecessary level of array.
pipelines/optimus/Optimus.wdl
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| @@ -222,5 +243,9 @@ workflow Optimus { | |||
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| # zarr | |||
| Array[File]? zarr_output_files = OptimusZarrConversion.zarr_output_files | |||
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| # fastqc | |||
| Array[Array[File]] fastqc_htmls = fastqc_output_htmls | |||
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Unless you really want Array[Array[File]] here it seems like you'd be better off with flatten(fastqc_output_htmls)
test/optimus/pr/ValidateOptimus.wdl
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| @@ -51,6 +52,14 @@ task ValidateOptimus { | |||
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| fi | |||
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| for htmlfile in ${sep=' ' fastqc_htmls}; do | |||
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I guess you can't easily check the zips here? The test could at least assert that the number of zip files generated is correct.
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@kbergin do we want to finish work on this? |
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I've made a ticket for us to rebase this and get these changes reviewed and merged in. |
Purpose
QA Inputs in SS2 and Optimus (and any future pipeline using fastqs as input)
Changes
Added FastQC task. For increased speed FastQC is run on only a subset of the fastq reads (can be set by inputs to task).