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Display more informations #451

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Sep 15, 2017
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Display more informations #451

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0c0ef37
Display all reference files used in the output
maxulysse Sep 14, 2017
32e02e3
Display all reference files used in the MultiQC report
maxulysse Sep 14, 2017
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27 changes: 27 additions & 0 deletions main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -1412,6 +1412,19 @@ process GenerateMultiQCconfig {
echo "- Step: "${step} >> multiqc_config.yaml
echo "- Tools: "${tools.join(", ")} >> multiqc_config.yaml
echo ${annotateString} >> multiqc_config.yaml
echo " acLoci : $referenceMap.acLoci" >> multiqc_config.yaml
echo " bwaIndex : "${referenceMap.bwaIndex.join(", ")} >> multiqc_config.yaml
echo " cosmic : $referenceMap.cosmic" >> multiqc_config.yaml
echo " cosmicIndex : $referenceMap.cosmicIndex" >> multiqc_config.yaml
echo " dbsnp : $referenceMap.dbsnp" >> multiqc_config.yaml
echo " dbsnpIndex : $referenceMap.dbsnpIndex" >> multiqc_config.yaml
echo " genomeDict : $referenceMap.genomeDict" >> multiqc_config.yaml
echo " genomeFile : $referenceMap.genomeFile" >> multiqc_config.yaml
echo " genomeIndex : $referenceMap.genomeIndex" >> multiqc_config.yaml
echo " intervals : $referenceMap.intervals" >> multiqc_config.yaml
echo " knownIndels : "${referenceMap.knownIndels.join(", ")} >> multiqc_config.yaml
echo " knownIndelsIndex: "${referenceMap.knownIndelsIndex.join(", ")} >> multiqc_config.yaml
echo " snpeffDb : ${params.genomes[params.genome].snpeffDb}" >> multiqc_config.yaml
echo "top_modules:" >> multiqc_config.yaml
echo "- 'fastqc'" >> multiqc_config.yaml
echo "- 'picard'" >> multiqc_config.yaml
Expand Down Expand Up @@ -1888,6 +1901,20 @@ def minimalInformationMessage() {
log.info "Step : " + step
if (tools) {log.info "Tools : " + tools.join(', ')}
if (annotateTools) {log.info "Annotate on : " + annotateTools.join(', ')}
log.info "Reference files used:"
log.info " acLoci : $referenceMap.acLoci"
log.info " bwaIndex : " + referenceMap.bwaIndex.join(',\n ')
log.info " cosmic : $referenceMap.cosmic"
log.info " cosmicIndex : $referenceMap.cosmicIndex"
log.info " dbsnp : $referenceMap.dbsnp"
log.info " dbsnpIndex : $referenceMap.dbsnpIndex"
log.info " genomeDict : $referenceMap.genomeDict"
log.info " genomeFile : $referenceMap.genomeFile"
log.info " genomeIndex : $referenceMap.genomeIndex"
log.info " intervals : $referenceMap.intervals"
log.info " knownIndels : " + referenceMap.knownIndels.join(',\n ')
log.info " knownIndelsIndex: " + referenceMap.knownIndelsIndex.join(',\n ')
log.info " snpeffDb : ${params.genomes[params.genome].snpeffDb}"
}

def nextflowMessage() {
Expand Down