From 0c0ef376e8296d5db992a274f7150fe27494a708 Mon Sep 17 00:00:00 2001 From: Maxime Garcia Date: Thu, 14 Sep 2017 16:45:59 +0200 Subject: [PATCH 1/2] Display all reference files used in the output --- main.nf | 14 ++++++++++++++ 1 file changed, 14 insertions(+) diff --git a/main.nf b/main.nf index af4887cc0..8e9ca8ada 100644 --- a/main.nf +++ b/main.nf @@ -1888,6 +1888,20 @@ 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 : ${params.genomes[params.genome].snpeffDb}" } def nextflowMessage() { From 32e02e38320c79ed37364ac49b4494b26eeaab2d Mon Sep 17 00:00:00 2001 From: Maxime Garcia Date: Thu, 14 Sep 2017 16:51:44 +0200 Subject: [PATCH 2/2] Display all reference files used in the MultiQC report --- main.nf | 13 +++++++++++++ 1 file changed, 13 insertions(+) diff --git a/main.nf b/main.nf index 8e9ca8ada..3f883aaa4 100644 --- a/main.nf +++ b/main.nf @@ -1412,6 +1412,19 @@ process GenerateMultiQCconfig { echo "- Step: "${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