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MultiQC optimisations for DIAMOND and Falco
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2 changed files with 7 additions and 3 deletions
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@ -37,8 +37,7 @@ run_modules:
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sp:
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diamond:
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contents: "diamond v"
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num_lines: 10
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fn_re: ".*.diamond.log$"
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fastqc/data:
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fn_re: ".*(fastqc|falco)_data.txt$"
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fastqc/zip:
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@ -270,7 +270,12 @@ workflow TAXPROFILER {
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ch_multiqc_files = ch_multiqc_files.mix(CUSTOM_DUMPSOFTWAREVERSIONS.out.mqc_yml.collect())
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if ( params.preprocessing_qc_tool == 'falco' ) {
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ch_multiqc_files = ch_multiqc_files.mix(FALCO.out.txt.collect{it[1]}.ifEmpty([]))
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// only mix in files acutally used by MultiQC
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ch_multiqc_files = ch_multiqc_files.mix(FALCO.out.txt
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.map { meta, reports -> reports }
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.flatten()
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.filter { path -> path.name.endsWith('_data.txt')}
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.ifEmpty([]))
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} else {
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ch_multiqc_files = ch_multiqc_files.mix(FASTQC.out.zip.collect{it[1]}.ifEmpty([]))
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}
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