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MultiQC optimisations for DIAMOND and Falco

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This commit is contained in:
James Fellows Yates 2023-04-20 15:57:57 +02:00
parent 0ed110c529
commit 1eb951715f
2 changed files with 7 additions and 3 deletions
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3
assets/multiqc_config.yml
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@ -37,8 +37,7 @@ run_modules:
sp: sp:
diamond: diamond:
contents: "diamond v" fn_re: ".*.diamond.log$"
num_lines: 10
fastqc/data: fastqc/data:
fn_re: ".*(fastqc|falco)_data.txt$" fn_re: ".*(fastqc|falco)_data.txt$"
fastqc/zip: fastqc/zip:

7
workflows/taxprofiler.nf
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@ -270,7 +270,12 @@ workflow TAXPROFILER {
ch_multiqc_files = ch_multiqc_files.mix(CUSTOM_DUMPSOFTWAREVERSIONS.out.mqc_yml.collect()) ch_multiqc_files = ch_multiqc_files.mix(CUSTOM_DUMPSOFTWAREVERSIONS.out.mqc_yml.collect())
if ( params.preprocessing_qc_tool == 'falco' ) { if ( params.preprocessing_qc_tool == 'falco' ) {
ch_multiqc_files = ch_multiqc_files.mix(FALCO.out.txt.collect{it[1]}.ifEmpty([])) // only mix in files acutally used by MultiQC
ch_multiqc_files = ch_multiqc_files.mix(FALCO.out.txt
.map { meta, reports -> reports }
.flatten()
.filter { path -> path.name.endsWith('_data.txt')}
.ifEmpty([]))
} else { } else {
ch_multiqc_files = ch_multiqc_files.mix(FASTQC.out.zip.collect{it[1]}.ifEmpty([])) ch_multiqc_files = ch_multiqc_files.mix(FASTQC.out.zip.collect{it[1]}.ifEmpty([]))
} }