#import re
#import os

die() { echo "$@" 1>&2 ; exit 1; } &&

mkdir multiqc_WDir &&

#set $configfile="F"

#for $i, $repeat in enumerate( $results )
    #set software_dir = os.path.join('multiqc_WDir', str($repeat.software_cond.software) + '_' + str($i))
    mkdir $software_dir &&
    #if str($repeat.software_cond.software) == "bamtools"
        
        #set $pattern = "Stats for BAM file\(s\)"
        
        
        #set file_paths = []
        #for $file in $repeat.software_cond.input:
            
        
        #set identifier = re.sub('[^\s\w\-]', '_', str($file.element_identifier))
    
            #set file_path = os.path.join($software_dir, str($identifier))
            
        
        #if $file_path in $file_paths
            #set $file_path += '_' + str($file_paths.count($file_path))
        #end if
        #set $file_paths += [$file_path]
        grep -Pq '$pattern' $file || die "Module '${repeat.software_cond.software}: '$pattern' not found in the file '$identifier'" &&
        ln -s '$file' '$file_path'  &&
    
        #end for
    
    
    #elif str($repeat.software_cond.software) == "bcftools"
        
        #set $pattern = "This file was produced by bcftools stats"
        
        
        #set file_paths = []
        #for $file in $repeat.software_cond.input:
            
        
        #set identifier = re.sub('[^\s\w\-]', '_', str($file.element_identifier))
    
            #set file_path = os.path.join($software_dir, str($identifier))
            
        
        #if $file_path in $file_paths
            #set $file_path += '_' + str($file_paths.count($file_path))
        #end if
        #set $file_paths += [$file_path]
        grep -Pq '$pattern' $file || die "Module '${repeat.software_cond.software}: '$pattern' not found in the file '$identifier'" &&
        ln -s '$file' '$file_path'  &&
    
        #end for
    
    
    #elif str($repeat.software_cond.software) == "bismark"
        
        #for $j, $repeat2 in enumerate( $repeat.software_cond.output )
            
        
        #set repeat_dir = os.path.join($software_dir, str($repeat2.type) + '_' + str($j))
        mkdir '$repeat_dir' &&
    
            #if str($repeat2.type) == "align"
                #for $file in $repeat2.input
                    
        
        #set identifier = re.sub('[^\s\w\-]', '_', str($file.element_identifier))
    
                    #set file_path = os.path.join($repeat_dir, str($identifier) + '_SE_report.txt')
                    ln -s '$file' '$file_path' &&
                #end for
            #elif str($repeat2.type) == "dedup"
                #for $file in $repeat2.input
                    
        
        #set identifier = re.sub('[^\s\w\-]', '_', str($file.element_identifier))
    
                    #set file_path = os.path.join($repeat_dir, str($identifier) + '_deduplication_report.txt')
                    ln -s '$file' '$file_path' &&
                #end for
            #elif str($repeat2.type) == "meth_extract"
                #for $file in $repeat2.input
                    
        
        #set identifier = re.sub('[^\s\w\-]', '_', str($file.element_identifier))
    
                    #set file_path = os.path.join($repeat_dir, str($identifier) + '_splitting_report.txt')
                    ln -s '$file' '$file_path' &&
                #end for
            #elif str($repeat2.type) == "m_bias"
                #for $file in $repeat2.input
                    
        
        #set identifier = re.sub('[^\s\w\-]', '_', str($file.element_identifier))
    
                    #set file_path = os.path.join($repeat_dir, str($identifier) + '_M-bias.txt')
                    ln -s '$file' '$file_path' &&
                #end for
            #elif str($repeat2.type) == "bam2nuc"
                #for $file in $repeat2.input
                    
        
        #set identifier = re.sub('[^\s\w\-]', '_', str($file.element_identifier))
    
                    #set file_path = os.path.join($repeat_dir, str($identifier) + '.nucleotide_stats.txt')
                    ln -s '$file' '$file_path' &&
                #end for
            #end if
        #end for
    
    #elif str($repeat.software_cond.software) == "bowtie2"
        
        #set $pattern = "% overall alignment rate"
        
        
        #set file_paths = []
        #for $file in $repeat.software_cond.input:
            
        
        #set identifier = re.sub('[^\s\w\-]', '_', str($file.element_identifier))
    
            #set file_path = os.path.join($software_dir, str($identifier))
            
        
        #if $file_path in $file_paths
            #set $file_path += '_' + str($file_paths.count($file_path))
        #end if
        #set $file_paths += [$file_path]
        grep -Pq '$pattern' $file || die "Module '${repeat.software_cond.software}: '$pattern' not found in the file '$identifier'" &&
        ln -s '$file' '$file_path'  &&
    
        #end for
    
    
    #elif str($repeat.software_cond.software) == "busco"
        
        ## Searches for files "short_summary_[samplename].txt"
        #for $file in $repeat.software_cond.input
            
        
        #set identifier = re.sub('[^\s\w\-]', '_', str($file.element_identifier))
    
            #set file_path = os.path.join($software_dir, 'short_summary_' + str($identifier))
            ln -s '$file' '$file_path' &&
        #end for
    
    #elif str($repeat.software_cond.software) == "cutadapt"
        
        #set $pattern = "This is cutadapt"
        #for $file in $repeat.software_cond.input
            
        
        #set identifier = re.sub('[^\s\w\-]', '_', str($file.element_identifier))
    
            #set file_path = os.path.join($software_dir, str($identifier) + '.txt')
            ln -s '$file' '$file_path' &&
            ## replace header for old cutadapt release
            sed -i.old 's/You are running/This is/' '$file_path' &&
            grep -q "$pattern" '$file_path' || die "'$pattern' or 'You are running cutadapt' not found in the file" &&
        #end for
    
    #elif str($repeat.software_cond.software) == "deeptools"
        
        #for $j, $repeat2 in enumerate( $repeat.software_cond.output )
            #if str($repeat2.type) == "bamPEFragmentSize"
                #set $pattern = "Frag."
                
        
        #set file_paths = []
        
        
        #set repeat_dir = os.path.join($software_dir, str($repeat2.type) + '_' + str($j))
        mkdir '$repeat_dir' &&
    
        #for $file in $repeat2.input
            #set identifier = re.sub('[^\s\w\-]', '_', str($file.element_identifier))
            #set file_path = os.path.join($repeat_dir, str($identifier))
            
        
        #if $file_path in $file_paths
            #set $file_path += '_' + str($file_paths.count($file_path))
        #end if
        #set $file_paths += [$file_path]
        grep -Pq '$pattern' $file || die "Module '${repeat.software_cond.software}: '$pattern' not found in the file '$identifier'" &&
        ln -s '$file' '$file_path'  &&
    
        #end for
    
            #elif str($repeat2.type) == "estimateReadFiltering"
                #set $pattern = "Internally-determined Duplicate"
                
        
        #set file_paths = []
        
        
        #set repeat_dir = os.path.join($software_dir, str($repeat2.type) + '_' + str($j))
        mkdir '$repeat_dir' &&
    
        #for $file in $repeat2.input
            #set identifier = re.sub('[^\s\w\-]', '_', str($file.element_identifier))
            #set file_path = os.path.join($repeat_dir, str($identifier))
            
        
        #if $file_path in $file_paths
            #set $file_path += '_' + str($file_paths.count($file_path))
        #end if
        #set $file_paths += [$file_path]
        grep -Pq '$pattern' $file || die "Module '${repeat.software_cond.software}: '$pattern' not found in the file '$identifier'" &&
        ln -s '$file' '$file_path'  &&
    
        #end for
    
            #elif str($repeat2.type) == "plotCoverageStdout"
                #set $pattern = "sample"
                
        
        #set file_paths = []
        
        
        #set repeat_dir = os.path.join($software_dir, str($repeat2.type) + '_' + str($j))
        mkdir '$repeat_dir' &&
    
        #for $file in $repeat2.input
            #set identifier = re.sub('[^\s\w\-]', '_', str($file.element_identifier))
            #set file_path = os.path.join($repeat_dir, str($identifier))
            
        
        #if $file_path in $file_paths
            #set $file_path += '_' + str($file_paths.count($file_path))
        #end if
        #set $file_paths += [$file_path]
        grep -Pq '$pattern' $file || die "Module '${repeat.software_cond.software}: '$pattern' not found in the file '$identifier'" &&
        ln -s '$file' '$file_path'  &&
    
        #end for
    
            #elif str($repeat2.type) == "plotCoverageOutRawCounts"
                #set $pattern = "#plotCoverage --outRawCounts"
                
        
        #set file_paths = []
        
        
        #set repeat_dir = os.path.join($software_dir, str($repeat2.type) + '_' + str($j))
        mkdir '$repeat_dir' &&
    
        #for $file in $repeat2.input
            #set identifier = re.sub('[^\s\w\-]', '_', str($file.element_identifier))
            #set file_path = os.path.join($repeat_dir, str($identifier))
            
        
        #if $file_path in $file_paths
            #set $file_path += '_' + str($file_paths.count($file_path))
        #end if
        #set $file_paths += [$file_path]
        grep -Pq '$pattern' $file || die "Module '${repeat.software_cond.software}: '$pattern' not found in the file '$identifier'" &&
        ln -s '$file' '$file_path'  &&
    
        #end for
    
            #elif str($repeat2.type) == "plotEnrichment"
                #set $pattern = "featureReadCount"
                
        
        #set file_paths = []
        
        
        #set repeat_dir = os.path.join($software_dir, str($repeat2.type) + '_' + str($j))
        mkdir '$repeat_dir' &&
    
        #for $file in $repeat2.input
            #set identifier = re.sub('[^\s\w\-]', '_', str($file.element_identifier))
            #set file_path = os.path.join($repeat_dir, str($identifier))
            
        
        #if $file_path in $file_paths
            #set $file_path += '_' + str($file_paths.count($file_path))
        #end if
        #set $file_paths += [$file_path]
        grep -Pq '$pattern' $file || die "Module '${repeat.software_cond.software}: '$pattern' not found in the file '$identifier'" &&
        ln -s '$file' '$file_path'  &&
    
        #end for
    
            #elif str($repeat2.type) == "plotFingerprintOutRawCounts"
                #set $pattern = "#plotFingerprint --outRawCounts"
                
        
        #set file_paths = []
        
        
        #set repeat_dir = os.path.join($software_dir, str($repeat2.type) + '_' + str($j))
        mkdir '$repeat_dir' &&
    
        #for $file in $repeat2.input
            #set identifier = re.sub('[^\s\w\-]', '_', str($file.element_identifier))
            #set file_path = os.path.join($repeat_dir, str($identifier))
            
        
        #if $file_path in $file_paths
            #set $file_path += '_' + str($file_paths.count($file_path))
        #end if
        #set $file_paths += [$file_path]
        grep -Pq '$pattern' $file || die "Module '${repeat.software_cond.software}: '$pattern' not found in the file '$identifier'" &&
        ln -s '$file' '$file_path'  &&
    
        #end for
    
            #end if
        #end for
    
    #elif str($repeat.software_cond.software) == "fastp"
        
        #set $pattern = "report_title"
        #for $file in $repeat.software_cond.input
            
        
        #set identifier = re.sub('[^\s\w\-]', '_', str($file.element_identifier))
    
            #set file_path = os.path.join($software_dir, str($identifier) + 'fastp.json')
            ln -s '$file' '$file_path' &&
            grep -q "$pattern" '$file_path' || die "'$pattern' or 'report_title' not found in the file" &&
        #end for
    
    #elif str($repeat.software_cond.software) == "fastqc"
        
    #for $j, $repeat2 in enumerate( $repeat.software_cond.output )
        
        
        #set repeat_dir = os.path.join($software_dir, str($repeat2.type) + '_' + str($j))
        mkdir '$repeat_dir' &&
    
        #if str($repeat2.type) == "data"
            #for $k, $file in enumerate($repeat2.input)
                #set file_dir = os.path.join($repeat_dir, 'file_' + str($k))
                #set file_path = os.path.join($file_dir, 'fastqc_data.txt')
                mkdir '$file_dir' &&
                ln -s '$file' '$file_path' &&
            #end for
        #elif str($repeat2.type) == "theoretical_gc"
            #for $file in $repeat2.input
                
        
        #set identifier = re.sub('[^\s\w\-]', '_', str($file.element_identifier))
    
                #set file_path = os.path.join($repeat_dir, str($identifier) + '_fastqc_theoretical_gc')
                ln -s '$file' '$file_path' &&
            #end for
        #end if
    #end for

    #elif str($repeat.software_cond.software) == "featureCounts"
        
        #for $file in $repeat.software_cond.input
            
        
        #set identifier = re.sub('[^\s\w\-]', '_', str($file.element_identifier))
    
            #set file_prefix = os.path.join($software_dir, str($identifier))
            if grep -qw Status '$file'; then
                ln -s '$file' '${file_prefix}.summary';
            else
                echo -e 'Status\t${identifier}' > '${file_prefix}.summary';
                cat '$file' >> '${file_prefix}.summary';
            fi &&
        #end for
    
    #elif str($repeat.software_cond.software) == "flexbar"
        
        #set $pattern = "flexible barcode and adapter removal"
        
        
        #set file_paths = []
        #for $file in $repeat.software_cond.input:
            
        
        #set identifier = re.sub('[^\s\w\-]', '_', str($file.element_identifier))
    
            #set file_path = os.path.join($software_dir, str($identifier))
            
        
        #if $file_path in $file_paths
            #set $file_path += '_' + str($file_paths.count($file_path))
        #end if
        #set $file_paths += [$file_path]
        grep -Pq '$pattern' $file || die "Module '${repeat.software_cond.software}: '$pattern' not found in the file '$identifier'" &&
        ln -s '$file' '$file_path'  &&
    
        #end for
    
    
    #elif str($repeat.software_cond.software) == "gatk"
        
        #for $j, $repeat2 in enumerate( $repeat.software_cond.output )
            #if str($repeat2.type) == "varianteval"
                #set $pattern = "#:GATKTable:TiTvVariantEvaluator"
                
        
        #set file_paths = []
        
        
        #set repeat_dir = os.path.join($software_dir, str($repeat2.type) + '_' + str($j))
        mkdir '$repeat_dir' &&
    
        #for $file in $repeat2.input
            #set identifier = re.sub('[^\s\w\-]', '_', str($file.element_identifier))
            #set file_path = os.path.join($repeat_dir, str($identifier))
            
        
        #if $file_path in $file_paths
            #set $file_path += '_' + str($file_paths.count($file_path))
        #end if
        #set $file_paths += [$file_path]
        grep -Pq '$pattern' $file || die "Module '${repeat.software_cond.software}: '$pattern' not found in the file '$identifier'" &&
        ln -s '$file' '$file_path'  &&
    
        #end for
    
            #elif str($repeat2.type) == "base_recalibrator"
                #set $pattern = "#:GATKTable:Arguments:Recalibration"
                
        
        #set file_paths = []
        
        
        #set repeat_dir = os.path.join($software_dir, str($repeat2.type) + '_' + str($j))
        mkdir '$repeat_dir' &&
    
        #for $file in $repeat2.input
            #set identifier = re.sub('[^\s\w\-]', '_', str($file.element_identifier))
            #set file_path = os.path.join($repeat_dir, str($identifier))
            
        
        #if $file_path in $file_paths
            #set $file_path += '_' + str($file_paths.count($file_path))
        #end if
        #set $file_paths += [$file_path]
        grep -Pq '$pattern' $file || die "Module '${repeat.software_cond.software}: '$pattern' not found in the file '$identifier'" &&
        ln -s '$file' '$file_path'  &&
    
        #end for
    
            #end if
        #end for
    
    #elif str($repeat.software_cond.software) == "hicup"
        #for $file in $repeat.software_cond.input
            
        
        #set identifier = re.sub('[^\s\w\-]', '_', str($file.element_identifier))
    
            #set file_path = os.path.join($software_dir, 'HiCUP_summary_report_' + str($identifier))
            ln -s '${file}' '$file_path' &&
        #end for
    #elif str($repeat.software_cond.software) == "hisat2"
        #set $pattern = "HISAT2 summary stats:"
        
        
        #set file_paths = []
        #for $file in $repeat.software_cond.input:
            
        
        #set identifier = re.sub('[^\s\w\-]', '_', str($file.element_identifier))
    
            #set file_path = os.path.join($software_dir, str($identifier))
            
        
        #if $file_path in $file_paths
            #set $file_path += '_' + str($file_paths.count($file_path))
        #end if
        #set $file_paths += [$file_path]
        grep -Pq '$pattern' $file || die "Module '${repeat.software_cond.software}: '$pattern' not found in the file '$identifier'" &&
        ln -s '$file' '$file_path'  &&
    
        #end for
    
    #elif str($repeat.software_cond.software) == "hicexplorer"
        #set $pattern = "Min rest. site distance"
        
        
        #set file_paths = []
        #for $file in $repeat.software_cond.input:
            
        
        #set identifier = re.sub('[^\s\w\-]', '_', str($file.element_identifier))
    
            #set file_path = os.path.join($software_dir, str($identifier))
            
        
        #if $file_path in $file_paths
            #set $file_path += '_' + str($file_paths.count($file_path))
        #end if
        #set $file_paths += [$file_path]
        grep -Pq '$pattern' $file || die "Module '${repeat.software_cond.software}: '$pattern' not found in the file '$identifier'" &&
        ln -s '$file' '$file_path'  &&
    
        #end for
    
    #elif str($repeat.software_cond.software) == "htseq"
        #set $pattern = "__too_low_aQual"
        
        
        #set file_paths = []
        #for $file in $repeat.software_cond.input:
            
        
        #set identifier = re.sub('[^\s\w\-]', '_', str($file.element_identifier))
    
            #set file_path = os.path.join($software_dir, str($identifier))
            
        
        #if $file_path in $file_paths
            #set $file_path += '_' + str($file_paths.count($file_path))
        #end if
        #set $file_paths += [$file_path]
        grep -Pq '$pattern' $file || die "Module '${repeat.software_cond.software}: '$pattern' not found in the file '$identifier'" &&
        ln -s '$file' '$file_path'  &&
    
        #end for
    
    #elif str($repeat.software_cond.software) == "kallisto"
        #set $pattern = "finding pseudoalignments for the reads"
        
        
        #set file_paths = []
        #for $file in $repeat.software_cond.input:
            
        
        #set identifier = re.sub('[^\s\w\-]', '_', str($file.element_identifier))
    
            #set file_path = os.path.join($software_dir, str($identifier))
            
        
        #if $file_path in $file_paths
            #set $file_path += '_' + str($file_paths.count($file_path))
        #end if
        #set $file_paths += [$file_path]
        grep -Pq '$pattern' $file || die "Module '${repeat.software_cond.software}: '$pattern' not found in the file '$identifier'" &&
        ln -s '$file' '$file_path'  &&
    
        #end for
    
    #elif str($repeat.software_cond.software) == "macs2"
        #set $pattern = "# This file is generated by MACS"
        #for $file in $repeat.software_cond.input
            
        
        #set identifier = re.sub('[^\s\w\-]', '_', str($file.element_identifier))
    
            #set file_path = os.path.join($software_dir, str($identifier) + '_peaks.xls')
            grep -q "$pattern" $file || die "'$pattern' not found in the file" &&
            ln -s '$file' '$file_path' &&
        #end for
    #elif str($repeat.software_cond.software) == "picard"
        
        #for $j, $repeat2 in enumerate( $repeat.software_cond.output )
            #if str($repeat2.type) == "alignment_metrics"
                #set $pattern = "picard.analysis.AlignmentSummaryMetrics"
                
        
        #set file_paths = []
        
        
        #set repeat_dir = os.path.join($software_dir, str($repeat2.type) + '_' + str($j))
        mkdir '$repeat_dir' &&
    
        #for $file in $repeat2.input
            #set identifier = re.sub('[^\s\w\-]', '_', str($file.element_identifier))
            #set file_path = os.path.join($repeat_dir, str($identifier))
            
        
        #if $file_path in $file_paths
            #set $file_path += '_' + str($file_paths.count($file_path))
        #end if
        #set $file_paths += [$file_path]
        grep -Pq '$pattern' $file || die "Module '${repeat.software_cond.software}: '$pattern' not found in the file '$identifier'" &&
        ln -s '$file' '$file_path'  &&
    
        #end for
    
            #elif str($repeat2.type) == "basedistributionbycycle"
                #set $pattern = "picard.analysis.BaseDistributionByCycleMetrics"
                
        
        #set file_paths = []
        
        
        #set repeat_dir = os.path.join($software_dir, str($repeat2.type) + '_' + str($j))
        mkdir '$repeat_dir' &&
    
        #for $file in $repeat2.input
            #set identifier = re.sub('[^\s\w\-]', '_', str($file.element_identifier))
            #set file_path = os.path.join($repeat_dir, str($identifier))
            
        
        #if $file_path in $file_paths
            #set $file_path += '_' + str($file_paths.count($file_path))
        #end if
        #set $file_paths += [$file_path]
        grep -Pq '$pattern' $file || die "Module '${repeat.software_cond.software}: '$pattern' not found in the file '$identifier'" &&
        ln -s '$file' '$file_path'  &&
    
        #end for
    
            #elif str($repeat2.type) == "gcbias"
                #set $pattern = "picard.analysis.GcBias"
                
        
        #set file_paths = []
        
        
        #set repeat_dir = os.path.join($software_dir, str($repeat2.type) + '_' + str($j))
        mkdir '$repeat_dir' &&
    
        #for $file in $repeat2.input
            #set identifier = re.sub('[^\s\w\-]', '_', str($file.element_identifier))
            #set file_path = os.path.join($repeat_dir, str($identifier))
            
        
        #if $file_path in $file_paths
            #set $file_path += '_' + str($file_paths.count($file_path))
        #end if
        #set $file_paths += [$file_path]
        grep -Pq '$pattern' $file || die "Module '${repeat.software_cond.software}: '$pattern' not found in the file '$identifier'" &&
        ln -s '$file' '$file_path'  &&
    
        #end for
    
            #elif str($repeat2.type) == "hsmetrics"
                #set $pattern = "picard.analysis.directed.HsMetrics"
                
        
        #set file_paths = []
        
        
        #set repeat_dir = os.path.join($software_dir, str($repeat2.type) + '_' + str($j))
        mkdir '$repeat_dir' &&
    
        #for $file in $repeat2.input
            #set identifier = re.sub('[^\s\w\-]', '_', str($file.element_identifier))
            #set file_path = os.path.join($repeat_dir, str($identifier))
            
        
        #if $file_path in $file_paths
            #set $file_path += '_' + str($file_paths.count($file_path))
        #end if
        #set $file_paths += [$file_path]
        grep -Pq '$pattern' $file || die "Module '${repeat.software_cond.software}: '$pattern' not found in the file '$identifier'" &&
        ln -s '$file' '$file_path'  &&
    
        #end for
    
            #elif str($repeat2.type) == "insertsize"
                #set $pattern = "picard.analysis.InsertSizeMetrics"
                
        
        #set file_paths = []
        
        
        #set repeat_dir = os.path.join($software_dir, str($repeat2.type) + '_' + str($j))
        mkdir '$repeat_dir' &&
    
        #for $file in $repeat2.input
            #set identifier = re.sub('[^\s\w\-]', '_', str($file.element_identifier))
            #set file_path = os.path.join($repeat_dir, str($identifier))
            
        
        #if $file_path in $file_paths
            #set $file_path += '_' + str($file_paths.count($file_path))
        #end if
        #set $file_paths += [$file_path]
        grep -Pq '$pattern' $file || die "Module '${repeat.software_cond.software}: '$pattern' not found in the file '$identifier'" &&
        ln -s '$file' '$file_path'  &&
    
        #end for
    
            #elif str($repeat2.type) == "markdups"
                #set $pattern = "MarkDuplicates"
                
        
        #set file_paths = []
        
        
        #set repeat_dir = os.path.join($software_dir, str($repeat2.type) + '_' + str($j))
        mkdir '$repeat_dir' &&
    
        #for $file in $repeat2.input
            #set identifier = re.sub('[^\s\w\-]', '_', str($file.element_identifier))
            #set file_path = os.path.join($repeat_dir, str($identifier))
            
        
        #if $file_path in $file_paths
            #set $file_path += '_' + str($file_paths.count($file_path))
        #end if
        #set $file_paths += [$file_path]
        grep -Pq '$pattern' $file || die "Module '${repeat.software_cond.software}: '$pattern' not found in the file '$identifier'" &&
        ln -s '$file' '$file_path'  &&
    
        #end for
    
            #elif str($repeat2.type) == "oxogmetrics"
                #set $pattern = "picard.analysis.CollectOxoGMetrics"
                
        
        #set file_paths = []
        
        
        #set repeat_dir = os.path.join($software_dir, str($repeat2.type) + '_' + str($j))
        mkdir '$repeat_dir' &&
    
        #for $file in $repeat2.input
            #set identifier = re.sub('[^\s\w\-]', '_', str($file.element_identifier))
            #set file_path = os.path.join($repeat_dir, str($identifier))
            
        
        #if $file_path in $file_paths
            #set $file_path += '_' + str($file_paths.count($file_path))
        #end if
        #set $file_paths += [$file_path]
        grep -Pq '$pattern' $file || die "Module '${repeat.software_cond.software}: '$pattern' not found in the file '$identifier'" &&
        ln -s '$file' '$file_path'  &&
    
        #end for
    
            #elif str($repeat2.type) == "pcr_metrics"
                #set $pattern = "picard.analysis.directed.TargetedPcrMetrics"
                
        
        #set file_paths = []
        
        
        #set repeat_dir = os.path.join($software_dir, str($repeat2.type) + '_' + str($j))
        mkdir '$repeat_dir' &&
    
        #for $file in $repeat2.input
            #set identifier = re.sub('[^\s\w\-]', '_', str($file.element_identifier))
            #set file_path = os.path.join($repeat_dir, str($identifier))
            
        
        #if $file_path in $file_paths
            #set $file_path += '_' + str($file_paths.count($file_path))
        #end if
        #set $file_paths += [$file_path]
        grep -Pq '$pattern' $file || die "Module '${repeat.software_cond.software}: '$pattern' not found in the file '$identifier'" &&
        ln -s '$file' '$file_path'  &&
    
        #end for
    
            #elif str($repeat2.type) == "rnaseqmetrics"
                #set $pattern = "Collect"
                
        
        #set file_paths = []
        
        
        #set repeat_dir = os.path.join($software_dir, str($repeat2.type) + '_' + str($j))
        mkdir '$repeat_dir' &&
    
        #for $file in $repeat2.input
            #set identifier = re.sub('[^\s\w\-]', '_', str($file.element_identifier))
            #set file_path = os.path.join($repeat_dir, str($identifier))
            
        
        #if $file_path in $file_paths
            #set $file_path += '_' + str($file_paths.count($file_path))
        #end if
        #set $file_paths += [$file_path]
        grep -Pq '$pattern' $file || die "Module '${repeat.software_cond.software}: '$pattern' not found in the file '$identifier'" &&
        ln -s '$file' '$file_path'  &&
    
        #end for
    
            #elif str($repeat2.type) == "rrbs_metrics"
                #set $pattern = "picard.analysis.RrbsSummaryMetrics"
                
        
        #set file_paths = []
        
        
        #set repeat_dir = os.path.join($software_dir, str($repeat2.type) + '_' + str($j))
        mkdir '$repeat_dir' &&
    
        #for $file in $repeat2.input
            #set identifier = re.sub('[^\s\w\-]', '_', str($file.element_identifier))
            #set file_path = os.path.join($repeat_dir, str($identifier))
            
        
        #if $file_path in $file_paths
            #set $file_path += '_' + str($file_paths.count($file_path))
        #end if
        #set $file_paths += [$file_path]
        grep -Pq '$pattern' $file || die "Module '${repeat.software_cond.software}: '$pattern' not found in the file '$identifier'" &&
        ln -s '$file' '$file_path'  &&
    
        #end for
    
            #elif str($repeat2.type) == "wgs_metrics"
                #set $pattern = "picard.analysis.CollectWgsMetrics$WgsMetrics"
                
        
        #set file_paths = []
        
        
        #set repeat_dir = os.path.join($software_dir, str($repeat2.type) + '_' + str($j))
        mkdir '$repeat_dir' &&
    
        #for $file in $repeat2.input
            #set identifier = re.sub('[^\s\w\-]', '_', str($file.element_identifier))
            #set file_path = os.path.join($repeat_dir, str($identifier))
            
        
        #if $file_path in $file_paths
            #set $file_path += '_' + str($file_paths.count($file_path))
        #end if
        #set $file_paths += [$file_path]
        grep -Pq '$pattern' $file || die "Module '${repeat.software_cond.software}: '$pattern' not found in the file '$identifier'" &&
        ln -s '$file' '$file_path'  &&
    
        #end for
    
            #end if
        #end for
    
    #elif str($repeat.software_cond.software) == "prokka"
        #set $pattern = "contigs:"
        
        
        #set file_paths = []
        #for $file in $repeat.software_cond.input:
            
        
        #set identifier = re.sub('[^\s\w\-]', '_', str($file.element_identifier))
    
            #set file_path = os.path.join($software_dir, str($identifier))
            
        
        #if $file_path in $file_paths
            #set $file_path += '_' + str($file_paths.count($file_path))
        #end if
        #set $file_paths += [$file_path]
        grep -Pq '$pattern' $file || die "Module '${repeat.software_cond.software}: '$pattern' not found in the file '$identifier'" &&
        ln -s '$file' '$file_path'  &&
    
        #end for
    
    #elif str($repeat.software_cond.software) == "pycoqc"
        
        #set $pattern = "\"pycoqc\":"
        
        
        #set file_paths = []
        #for $file in $repeat.software_cond.input:
            
        
        #set identifier = re.sub('[^\s\w\-]', '_', str($file.element_identifier))
    
            #set file_path = os.path.join($software_dir, str($identifier))
            
        
        #if $file_path in $file_paths
            #set $file_path += '_' + str($file_paths.count($file_path))
        #end if
        #set $file_paths += [$file_path]
        grep -Pq '$pattern' $file || die "Module '${repeat.software_cond.software}: '$pattern' not found in the file '$identifier'" &&
        ln -s '$file' '$file_path'  &&
    
        #end for
    
    
    #elif str($repeat.software_cond.software) == "qualimap"
        
        #for $file in $repeat.software_cond.input
            #if re.search("genome_results", str($file.element_identifier))
                sample="\$(grep 'bam file = ' $file | sed 's/bam file = //g' | sed 's: ::g')" &&
                dir_name="$software_dir/\${sample}" &&
                mkdir -p \${dir_name} &&
                filepath_1="\${dir_name}/genome_results.txt" &&
                ln -sf '$file' \${filepath_1} &&
            #elif re.search("coverage_histogram", str($file.element_identifier))
                nested_dir_name="\${dir_name}/raw_data_qualimapReport/" &&
                mkdir -p \${nested_dir_name} &&
                filepath_2="\${nested_dir_name}/coverage_histogram.txt" &&
                ln -sf '$file' \${filepath_2} &&
            #elif re.search("gc-content_distribution", str($file.element_identifier))
                nested_dir_name="\${dir_name}/raw_data_qualimapReport/" &&
                mkdir -p \${nested_dir_name} &&
                filepath_3="\${nested_dir_name}/mapped_reads_gc-content_distribution.txt" &&
                ln -sf '$file' \${filepath_3} &&
            #else
                #pass
            #end if
        #end for
    
    #elif str($repeat.software_cond.software) == "quast"
        #for $k, $file in enumerate($repeat.software_cond.input)
            #set file_dir = os.path.join($software_dir, 'file_' + str($k))
            #set file_path = os.path.join($file_dir, 'report.tsv')
            mkdir '$file_dir' &&
            ln -s '$file' '$file_path' &&
        #end for
    #elif str($repeat.software_cond.software) == "rsem"
        #for $file in $repeat.software_cond.input
            
        
        #set identifier = re.sub('[^\s\w\-]', '_', str($file.element_identifier))
    
            #set file_path = os.path.join($software_dir, str($identifier) + '.cnt')
            ln -s '$file' '$file_path' &&
        #end for
    #elif str($repeat.software_cond.software) == "rseqc"
        
        #for $j, $repeat2 in enumerate( $repeat.software_cond.output )
            
        
        #set repeat_dir = os.path.join($software_dir, str($repeat2.type.type) + '_' + str($j))
        mkdir '$repeat_dir' &&
    
            #if str($repeat2.type.type) == "bam_stat"
                #set $pattern = "Proper-paired reads map to different chrom:"
                
        
        #set file_paths = []
        #for $file in $repeat2.type.input
            #set identifier = re.sub('[^\s\w\-]', '_', str($file.element_identifier))
            #set file_path = os.path.join($repeat_dir, str($identifier))
            
        
        #if $file_path in $file_paths
            #set $file_path += '_' + str($file_paths.count($file_path))
        #end if
        #set $file_paths += [$file_path]
        grep -Pq '$pattern' $file || die "Module '${repeat.software_cond.software}: '$pattern' not found in the file '$identifier'" &&
        ln -s '$file' '$file_path'  &&
    
        #end for
    
            #elif str($repeat2.type.type) == "gene_body_coverage"
                #for $k, $file in enumerate($repeat2.type.input)
                    #set file_path = os.path.join($repeat_dir, 'file_' + str($k) + '.geneBodyCoverage.txt')
                    ln -s '$file' '$file_path' &&
                #end for
            #elif str($repeat2.type.type) == "inner_distance"
                #for $k, $file in enumerate($repeat2.type.input)
                    #set file_path = os.path.join($repeat_dir, 'file_' + str($k) + '.inner_distance_freq.txt')
                    ln -s '${file}' '$file_path' &&
                #end for
            #elif str($repeat2.type.type) == "junction_annotation"
                #set $pattern = "Partial Novel Splicing Junctions:"
                
        
        #set file_paths = []
        #for $file in $repeat2.type.input
            #set identifier = re.sub('[^\s\w\-]', '_', str($file.element_identifier))
            #set file_path = os.path.join($repeat_dir, str($identifier))
            
        
        #if $file_path in $file_paths
            #set $file_path += '_' + str($file_paths.count($file_path))
        #end if
        #set $file_paths += [$file_path]
        grep -Pq '$pattern' $file || die "Module '${repeat.software_cond.software}: '$pattern' not found in the file '$identifier'" &&
        ln -s '$file' '$file_path'  &&
    
        #end for
    
            #elif str($repeat2.type.type) == "read_gc"
                #for $k, $file in enumerate($repeat2.type.input)
                    #set file_path = os.path.join($repeat_dir, 'file_' + str($k) + '.GC.xls')
                    ln -s '$file' '$file_path' &&
                #end for
            #elif str($repeat2.type.type) == "junction_saturation"
                #for $k, $file in enumerate($repeat2.type.input)
                #set file_path = os.path.join($repeat_dir, 'file_' + str($k) + '.junctionSaturation_plot.r')
                    ln -s '${file}' '$file_path' &&
                #end for
            #elif str($repeat2.type.type) == "read_distribution"
                #set $pattern = "Group               Total_bases         Tag_count           Tags/Kb"
                
        
        #set file_paths = []
        #for $file in $repeat2.type.input
            #set identifier = re.sub('[^\s\w\-]', '_', str($file.element_identifier))
            #set file_path = os.path.join($repeat_dir, str($identifier))
            
        
        #if $file_path in $file_paths
            #set $file_path += '_' + str($file_paths.count($file_path))
        #end if
        #set $file_paths += [$file_path]
        grep -Pq '$pattern' $file || die "Module '${repeat.software_cond.software}: '$pattern' not found in the file '$identifier'" &&
        ln -s '$file' '$file_path'  &&
    
        #end for
    
            #elif str($repeat2.type.type) == "read_duplication_pos"
                #for $k, $file in enumerate($repeat2.type.input)
                    #set file_path = os.path.join($repeat_dir, 'file_' + str($k) + '.pos.DupRate.xls')
                    ln -s '$file' '$file_path' &&
                #end for
            #elif str($repeat2.type.type) == "infer_experiment"
                #set $pattern = "Fraction of reads explained by"
                #for $file in $repeat2.type.input
                    
        
        #set identifier = re.sub('[^\s\w\-]', '_', str($file.element_identifier))
    
                    #set file_path = os.path.join($repeat_dir, str($identifier))
                    grep -q "$pattern" $file || die "'$pattern' not found in the file" &&
                    ln -s '$file' '$file_path' &&
                #end for
            #end if
        #end for
    
    #elif str($repeat.software_cond.software) == "salmon"
        
        #for $j, $repeat2 in enumerate( $repeat.software_cond.output )
            
        
        #set repeat_dir = os.path.join($software_dir, str($repeat2.type.type) + '_' + str($j))
        mkdir '$repeat_dir' &&
    
            #if str($repeat2.type.type) == "meta"
                #for $k, $file in enumerate($repeat2.type.input)
                    #set file_dir = os.path.join($repeat_dir, 'file_' + str($k))
                    #set file_path = os.path.join($file_dir, 'meta_info.json')
                    mkdir '$file_dir' &&
                    ln -s '$file' '$file_path' &&
                #end for
            #elif str($repeat2.type.type) == "fld"
                #for $k, $file in enumerate($repeat2.type.input)
                    #set file_dir = os.path.join($repeat_dir, 'file_' + str($k))
                    #set file_path = os.path.join($file_dir,'flenDist.txt')
                    mkdir '$file_dir' &&
                    ln -s '$file' '$file_path' &&
                #end for
            #end if
        #end for
    
    #elif str($repeat.software_cond.software) == "samblaster"
        #set $pattern = "samblaster: Version"
        
        
        #set file_paths = []
        #for $file in $repeat.software_cond.input:
            
        
        #set identifier = re.sub('[^\s\w\-]', '_', str($file.element_identifier))
    
            #set file_path = os.path.join($software_dir, str($identifier))
            
        
        #if $file_path in $file_paths
            #set $file_path += '_' + str($file_paths.count($file_path))
        #end if
        #set $file_paths += [$file_path]
        grep -Pq '$pattern' $file || die "Module '${repeat.software_cond.software}: '$pattern' not found in the file '$identifier'" &&
        ln -s '$file' '$file_path'  &&
    
        #end for
    
    #elif str($repeat.software_cond.software) == "samtools"
        
        #for $j, $repeat2 in enumerate( $repeat.software_cond.output )
            
        
        #set repeat_dir = os.path.join($software_dir, str($repeat2.type.type) + '_' + str($j))
        mkdir '$repeat_dir' &&
    
            #if str($repeat2.type.type) == "stats"
                #set $pattern = "This file was produced by samtools stats"
                
        
        #set file_paths = []
        #for $file in $repeat2.type.input
            #set identifier = re.sub('[^\s\w\-]', '_', str($file.element_identifier))
            #set file_path = os.path.join($repeat_dir, str($identifier))
            
        
        #if $file_path in $file_paths
            #set $file_path += '_' + str($file_paths.count($file_path))
        #end if
        #set $file_paths += [$file_path]
        grep -Pq '$pattern' $file || die "Module '${repeat.software_cond.software}: '$pattern' not found in the file '$identifier'" &&
        ln -s '$file' '$file_path'  &&
    
        #end for
    
            #elif str($repeat2.type.type) == "flagstat"
                #set $pattern = "in total \(QC-passed reads \+ QC-failed reads\)"
                
        
        #set file_paths = []
        #for $file in $repeat2.type.input
            #set identifier = re.sub('[^\s\w\-]', '_', str($file.element_identifier))
            #set file_path = os.path.join($repeat_dir, str($identifier))
            
        
        #if $file_path in $file_paths
            #set $file_path += '_' + str($file_paths.count($file_path))
        #end if
        #set $file_paths += [$file_path]
        grep -Pq '$pattern' $file || die "Module '${repeat.software_cond.software}: '$pattern' not found in the file '$identifier'" &&
        ln -s '$file' '$file_path'  &&
    
        #end for
    
            #elif str($repeat2.type.type) == "idxstats"
                #for $file in $repeat2.type.input
                    
        
        #set identifier = re.sub('[^\s\w\-]', '_', str($file.element_identifier))
    
                    #set file_path = os.path.join($repeat_dir, str($identifier) + '_idxstat')
                    ln -s '$file' '$file_path' &&
                #end for
            #elif str($repeat2.type.type) == "rmdup"
                #set $pattern = "\[bam_rmdup"
                
        
        #set file_paths = []
        #for $file in $repeat2.type.input
            #set identifier = re.sub('[^\s\w\-]', '_', str($file.element_identifier))
            #set file_path = os.path.join($repeat_dir, str($identifier))
            
        
        #if $file_path in $file_paths
            #set $file_path += '_' + str($file_paths.count($file_path))
        #end if
        #set $file_paths += [$file_path]
        grep -Pq '$pattern' $file || die "Module '${repeat.software_cond.software}: '$pattern' not found in the file '$identifier'" &&
        ln -s '$file' '$file_path'  &&
    
        #end for
    
            #end if
        #end for
    
    #elif str($repeat.software_cond.software) == "slamdunk"
        #set $pattern = "# slamdunk"
        
        
        #set file_paths = []
        #for $file in $repeat.software_cond.input:
            
        
        #set identifier = re.sub('[^\s\w\-]', '_', str($file.element_identifier))
    
            #set file_path = os.path.join($software_dir, str($identifier))
            
        
        #if $file_path in $file_paths
            #set $file_path += '_' + str($file_paths.count($file_path))
        #end if
        #set $file_paths += [$file_path]
        grep -Pq '$pattern' $file || die "Module '${repeat.software_cond.software}: '$pattern' not found in the file '$identifier'" &&
        ln -s '$file' '$file_path'  &&
    
        #end for
    
    #elif str($repeat.software_cond.software) == "snpeff"
        #set $pattern = "SnpEff_version"
        
        
        #set file_paths = []
        #for $file in $repeat.software_cond.input:
            
        
        #set identifier = re.sub('[^\s\w\-]', '_', str($file.element_identifier))
    
            #set file_path = os.path.join($software_dir, str($identifier))
            
        
        #if $file_path in $file_paths
            #set $file_path += '_' + str($file_paths.count($file_path))
        #end if
        #set $file_paths += [$file_path]
        grep -Pq '$pattern' $file || die "Module '${repeat.software_cond.software}: '$pattern' not found in the file '$identifier'" &&
        ln -s '$file' '$file_path'  &&
    
        #end for
    
    #elif str($repeat.software_cond.software) == "sortmerna"
        #set $pattern = "Minimal SW score based on E-value"
        
        
        #set file_paths = []
        #for $file in $repeat.software_cond.input:
            
        
        #set identifier = re.sub('[^\s\w\-]', '_', str($file.element_identifier))
    
            #set file_path = os.path.join($software_dir, str($identifier))
            
        
        #if $file_path in $file_paths
            #set $file_path += '_' + str($file_paths.count($file_path))
        #end if
        #set $file_paths += [$file_path]
        grep -Pq '$pattern' $file || die "Module '${repeat.software_cond.software}: '$pattern' not found in the file '$identifier'" &&
        ln -s '$file' '$file_path'  &&
    
        #end for
    
    #else if str($repeat.software_cond.software) == "star":
        
        #for $j, $repeat2 in enumerate( $repeat.software_cond.output )
            
        
        #set repeat_dir = os.path.join($software_dir, str($repeat2.type.type) + '_' + str($j))
        mkdir '$repeat_dir' &&
    
            #if str($repeat2.type.type) == "log"
                #for $file in $repeat2.type.input
                    
        
        #set identifier = re.sub('[^\s\w\-]', '_', str($file.element_identifier))
    
                    #set file_path = os.path.join($repeat_dir, str($identifier) + '_Log.final.out')
                    ln -s '$file' '$file_path' &&
                #end for
            #elif str($repeat2.type.type) == "genecounts"
                #for $file in $repeat2.type.input
                    
        
        #set identifier = re.sub('[^\s\w\-]', '_', str($file.element_identifier))
    
                    #set file_path = os.path.join($repeat_dir, str($identifier) + '_ReadsPerGene.out.tab')
                    ln -s '$file' '$file_path' &&
                #end for
            #end if
        #end for
    
    #elif str($repeat.software_cond.software) == "tophat"
        #for $file in $repeat.software_cond.input
            
        
        #set identifier = re.sub('[^\s\w\-]', '_', str($file.element_identifier))
    
            #set file_path = os.path.join($software_dir, str($identifier) + 'align_summary.txt')
            ln -s '$file' '$file_path' &&
        #end for
    #elif str($repeat.software_cond.software) == "trimmomatic"
        
        
    #set $pattern = "Trimmomatic"
    
        
        #set file_paths = []
        #for $file in $repeat.software_cond.input:
            
        
        #set identifier = re.sub('[^\s\w\-]', '_', str($file.element_identifier))
    
            #set file_path = os.path.join($software_dir, str($identifier))
            
        
        #if $file_path in $file_paths
            #set $file_path += '_' + str($file_paths.count($file_path))
        #end if
        #set $file_paths += [$file_path]
        grep -Pq '$pattern' $file || die "Module '${repeat.software_cond.software}: '$pattern' not found in the file '$identifier'" &&
        ln -s '$file' '$file_path'  &&
    
        #end for
    

    #elif str($repeat.software_cond.software) == "vcftools"
        
        #for $j, $repeat2 in enumerate( $repeat.software_cond.output )
            
        
        #set repeat_dir = os.path.join($software_dir, str($repeat2.type.type) + '_' + str($j))
        mkdir '$repeat_dir' &&
    
            #if str($repeat2.type.type) == "relatedness2"
                #for $file in $repeat2.type.input
                    
        
        #set identifier = re.sub('[^\s\w\-]', '_', str($file.element_identifier))
    
                    #set file_path = os.path.join($repeat_dir, str($identifier) + '.relatedness2')
                    ln -s '$file' '$file_path' &&
                #end for
            #elif str($repeat2.type) == "tstv_by_count"
                #for $file in $repeat2.type.input
                    
        
        #set identifier = re.sub('[^\s\w\-]', '_', str($file.element_identifier))
    
                    #set file_path = os.path.join($repeat_dir, str($identifier) + '.TsTv.count')
                    ln -s '$file' '$file_path' &&
                #end for
            #elif str($repeat2.type) == "tstv_by_qual"
                #for $file in $repeat2.type.input
                    
        
        #set identifier = re.sub('[^\s\w\-]', '_', str($file.element_identifier))
    
                    #set file_path = os.path.join($repeat_dir, str($identifier) + '.TsTv.qual')
                    ln -s '$file' '$file_path' &&
                #end for
            #elif str($repeat2.type) == "tstv_summary"
                #for $file in $repeat2.type.input
                    
        
        #set identifier = re.sub('[^\s\w\-]', '_', str($file.element_identifier))
    
                    #set file_path = os.path.join($repeat_dir, str($identifier) + '.TsTv.summary')
                    ln -s '$file' '$file_path' &&
                #end for
            #end if
        #end for
    
    #elif str($repeat.software_cond.software) == "kraken"
        
        #set $pattern = "^\s{0,2}(\d{1,3}\.\d{1,2})\t(\d+)\t(\d+)\t((\d+)\t(\d+)\t)?([URDKPCOFGS-]\d{0,2})\t(\d+)(\s+)[root|unclassified]"
        
        
        #set file_paths = []
        #for $file in $repeat.software_cond.input:
            
        
        #set identifier = re.sub('[^\s\w\-]', '_', str($file.element_identifier))
    
            #set file_path = os.path.join($software_dir, str($identifier))
            
        
        #if $file_path in $file_paths
            #set $file_path += '_' + str($file_paths.count($file_path))
        #end if
        #set $file_paths += [$file_path]
        grep -Pq '$pattern' $file || die "Module '${repeat.software_cond.software}: '$pattern' not found in the file '$identifier'" &&
        ln -s '$file' '$file_path'  &&
    
        #end for
    
    
    #elif str($repeat.software_cond.software) == "diamond"
        
        #for $file in $repeat.software_cond.input
            
        
        #set identifier = re.sub('[^\s\w\-]', '_', str($file.element_identifier))
    
            #set file_path = os.path.join($software_dir, 'diamond.log')
            ln -s '$file' '$file_path' &&
        #end for
    
    #elif str($repeat.software_cond.software) == "bakta"
        
        #set $pattern = "Bakta:"
        #for $file in $repeat.software_cond.input
            
        
        #set identifier = re.sub('[^\s\w\-]', '_', str($file.element_identifier))
    
            #set file_path = os.path.join($software_dir, str($identifier) + '.txt')
            ln -s '$file' '$file_path' &&
        #end for
    
    #elif str($repeat.software_cond.software) == "freyja"
        
        #set $pattern = "summarized\t\["
        #for $file in $repeat.software_cond.input
            
        
        #set identifier = re.sub('[^\s\w\-]', '_', str($file.element_identifier))
    
            #set file_path = os.path.join($software_dir, str($identifier) + '.tsv')
            ln -s '$file' '$file_path' &&
        #end for
    
    #elif str($repeat.software_cond.software) == "checkm"
        
        #set $pattern = ".*Bin Id(?:\t| {3,})Marker lineage(?:\t| {3,})# genomes(?:\t| {3,})# markers(?:\t| {3,})# marker sets.*"
        #for $file in $repeat.software_cond.input
            
        
        #set identifier = re.sub('[^\s\w\-]', '_', str($file.element_identifier))
    
            #set file_path = os.path.join($software_dir, 'output_file')
            ln -s '$file' '$file_path' &&
        #end for
    
    #elif str($repeat.software_cond.software) == "pairtools"
        
        #set $pattern = "total_single_sided_mapped"
        #set file_paths = []
        #for $file in $repeat.software_cond.input:
            
        
        #set identifier = re.sub('[^\s\w\-]', '_', str($file.element_identifier))
    
            #set file_path = os.path.join($software_dir, str($identifier))
            #if $file_path in $file_paths
                #set $file_path += '_' + str($file_paths.count($file_path))
            #end if
            #set $file_paths += [$file_path]
            grep -Pzq "(?s)(?=.*total_single_sided_mapped\t)(?=.*cis\t)(?=.*trans\t)(?=.*pair_types/)" $file || die "Module '${repeat.software_cond.software}: '$pattern' not found in the file '$identifier'" &&
            ln -s '$file' '$file_path'  &&
        #end for
    
    #elif str($repeat.software_cond.software) == "porechop"
        
        #set $pattern = "Looking for known adapter sets"
        
        
        #set file_paths = []
        #for $file in $repeat.software_cond.input:
            
        
        #set identifier = re.sub('[^\s\w\-]', '_', str($file.element_identifier))
    
            #set file_path = os.path.join($software_dir, str($identifier))
            
        
        #if $file_path in $file_paths
            #set $file_path += '_' + str($file_paths.count($file_path))
        #end if
        #set $file_paths += [$file_path]
        grep -Pq '$pattern' $file || die "Module '${repeat.software_cond.software}: '$pattern' not found in the file '$identifier'" &&
        ln -s '$file' '$file_path'  &&
    
        #end for
    
    
    #elif str($repeat.software_cond.software) == "snippy"
        
        #set $pattern = "snippy|ID\tLENGTH\tALIGNED\tUNALIGNED\tVARIANT\tHET\tMASKED\tLOWCOV"
        
        
        #set file_paths = []
        #for $file in $repeat.software_cond.input:
            
        
        #set identifier = re.sub('[^\s\w\-]', '_', str($file.element_identifier))
    
            #set file_path = os.path.join($software_dir, str($identifier))
            
        
        #if $file_path in $file_paths
            #set $file_path += '_' + str($file_paths.count($file_path))
        #end if
        #set $file_paths += [$file_path]
        grep -Pq '$pattern' $file || die "Module '${repeat.software_cond.software}: '$pattern' not found in the file '$identifier'" &&
        ln -s '$file' '$file_path'  &&
    
        #end for
    
    
    #elif str($repeat.software_cond.software) == "metaphlan"
        
        #set $pattern = "#clade_name\tNCBI_tax_id\trelative_abundance\t"
        #for $file in $repeat.software_cond.input
            
        
        #set identifier = re.sub('[^\s\w\-]', '_', str($file.element_identifier))
    
            #set file_path = os.path.join($software_dir, str($identifier) + '.txt')
            ln -s '$file' '$file_path' &&
        #end for
    
    #elif str($repeat.software_cond.software) == "bbduk"
        
        #set $pattern = "Executing jgi\.BBDuk"
        
        
        #set file_paths = []
        #for $file in $repeat.software_cond.input:
            
        
        #set identifier = re.sub('[^\s\w\-]', '_', str($file.element_identifier))
    
            #set file_path = os.path.join($software_dir, str($identifier))
            
        
        #if $file_path in $file_paths
            #set $file_path += '_' + str($file_paths.count($file_path))
        #end if
        #set $file_paths += [$file_path]
        grep -Pq '$pattern' $file || die "Module '${repeat.software_cond.software}: '$pattern' not found in the file '$identifier'" &&
        ln -s '$file' '$file_path'  &&
    
        #end for
    
    
    #elif str($repeat.software_cond.software) == "megahit"
        
        #set $pattern = " - MEGAHIT v"
        
        
        #set file_paths = []
        #for $file in $repeat.software_cond.input:
            
        
        #set identifier = re.sub('[^\s\w\-]', '_', str($file.element_identifier))
    
            #set file_path = os.path.join($software_dir, str($identifier))
            
        
        #if $file_path in $file_paths
            #set $file_path += '_' + str($file_paths.count($file_path))
        #end if
        #set $file_paths += [$file_path]
        grep -Pq '$pattern' $file || die "Module '${repeat.software_cond.software}: '$pattern' not found in the file '$identifier'" &&
        ln -s '$file' '$file_path'  &&
    
        #end for
    
    
    #elif str($repeat.software_cond.software) == "nonpareil"
        
        #set $pattern = "LRstar"
        #for $file in $repeat.software_cond.input
            
        
        #set identifier = re.sub('[^\s\w\-]', '_', str($file.element_identifier))
    
            #set file_path = os.path.join($software_dir, str($identifier) + '.json')
            ln -s '$file' '$file_path' &&
        #end for
    
    #elif str($repeat.software_cond.software) == "gtdbtk"
        
        #set $pattern = "user_genome\tclassification\tclosest_genome_reference\tclosest_genome_reference_radius\tclosest_genome_taxonomy\tclosest_genome_ani"
        
        
        #set file_paths = []
        #for $file in $repeat.software_cond.input:
            
        
        #set identifier = re.sub('[^\s\w\-]', '_', str($file.element_identifier))
    
            #set file_path = os.path.join($software_dir, str($identifier))
            
        
        #if $file_path in $file_paths
            #set $file_path += '_' + str($file_paths.count($file_path))
        #end if
        #set $file_paths += [$file_path]
        grep -Pq '$pattern' $file || die "Module '${repeat.software_cond.software}: '$pattern' not found in the file '$identifier'" &&
        ln -s '$file' '$file_path'  &&
    
        #end for
    
    
    #elif str($repeat.software_cond.software) == "sambamba"
        
        #set $pattern = "finding positions of the duplicate reads in the file"
        
        
        #set file_paths = []
        #for $file in $repeat.software_cond.input:
            
        
        #set identifier = re.sub('[^\s\w\-]', '_', str($file.element_identifier))
    
            #set file_path = os.path.join($software_dir, str($identifier))
            
        
        #if $file_path in $file_paths
            #set $file_path += '_' + str($file_paths.count($file_path))
        #end if
        #set $file_paths += [$file_path]
        grep -Pq '$pattern' $file || die "Module '${repeat.software_cond.software}: '$pattern' not found in the file '$identifier'" &&
        ln -s '$file' '$file_path'  &&
    
        #end for
    
    
    #else if str($repeat.software_cond.software) == "custom_content":
        #set $configfile = "T"
        #for $j, $file in enumerate( $repeat.software_cond.input )
            #set file_path = os.path.join($software_dir, 'file_' + str($i) + '_' + str($j))
            ln -s '$file' '$file_path' &&
            more $file &&
        #end for
    #end if
#end for

#if str($image_content_input) != "None"
    
        #for $file in $image_content_input
            #set identifier = re.sub('[^\s\w\-\.]', '_', str($file.element_identifier))
            #set file_parts = str($file.element_identifier).rsplit('.', 1)
            #set file_path = os.path.join('multiqc_WDir/', file_parts[0] + '_mqc.' + str($file.ext))
            ln -s '$file' '$file_path' &&
        #end for
    
#end if

multiqc multiqc_WDir
--filename 'report'

#if str($title)
    --title '$title'
#end if
#if str($comment)
    --comment '$comment'
#end if

$flat
$export

#if $configfile == "T"
    --config '$multiqc_config'
#end if

&&
mkdir -p ./plots &&
ls -l ./report_data/ &&
##cat ./report_data/multiqc_busco.txt &&
cp ./report_data/*plot*.txt ./plots/ | true ## don't fail if no plot files are generated