main.nf

#!/usr/bin/env nextflow
/*
vim: syntax=groovy
-*- mode: groovy;-*-
========================================================================================
         ELEMENTO - MELNICK LABS ||  ATAC-SEQ   BEST   PRACTICE
========================================================================================
#### Authors
Ashley Stephen Doane <asd2007@med.cornell.edu>

*/
//params.index = '/home/asd2007/Scripts/nf/fripflow/sindex.tsv'



version = 1.2

// SET PARAMS

params.name = 'ecadd4547'
params.index = 'sampleIndex.csv'
params.outdir = "$baseDir/results"
params.name = false
params.project = false
params.genome = ''
params.genomes = []
params.fasta = params.genome ? params.genomes[ params.genome ].fasta ?: false : false
params.bwa_index = params.genome ? params.genomes[ params.genome ].bwa ?: false : false
params.blacklist = params.genome ? params.genomes[ params.genome ].blacklist ?: false : false
params.black = params.genome ? params.genomes[ params.genome ].BLACK ?: false : false
params.notrim = false
params.saveReference = true
params.saveTrimmed = false
params.saveAlignedIntermediates = false
params.broad = false
params.outdir = './results'
params.email = 'ashley.doane@gmail.com'
params.lncaprefpeak = "$baseDir/data/lncapPeak.narrowPeak" 
params.bcellrefpeak = "$baseDir/data/gcb.tn5.broadPeak" 
params.bt2_index = params.genome ? params.genomes[ params.genome ].bt2 ?: false : false
params.species = params.genome ? params.genomes[ params.genome ].spec ?: false : false
params.picardconfig = params.genome ? params.genomes[ params.genome ].picardconf ?: false : false
params.DNASE = params.genome ? params.genomes[ params.genome ].DNASE ?: false : false
params.TSS_ENRICH = params.genome ? params.genomes[ params.genome ].TSS_ENRICH ?: false : false
params.PROM = params.genome ? params.genomes[ params.genome ].PROM ?: false : false
params.ENH = params.genome ? params.genomes[ params.genome ].ENH ?: false : false
params.REG2MAP = params.genome ? params.genomes[ params.genome ].REG2MAP ?: false : false
params.ROADMAP_META = params.genome ? params.genomes[ params.genome ].ROADMAP_META ?: false : false
params.REF = params.genome ? params.genomes[ params.genome ].REF ?: false : false
params.REG2MAP_BED = params.genome ? params.genomes[ params.genome ].REG2MAP_BED ?: false : false
params.chrsz = params.genome ? params.genomes[ params.genome ].chrsz ?: false : false
params.encodedhs = params.genome ? params.genomes[ params.genome ].ENCODEDHS ?: false : false
       //params.picardconfig="/athena/elementolab/scratch/asd2007/reference/hg38/picardmetrics.conf"


if( params.bwa_index ){
    bwa_index = Channel
        .fromPath(params.bwa_index)
        .ifEmpty { exit 1, "BWA index not found: ${params.bwa_index}" }
} else if ( params.fasta ){
    fasta = file(params.fasta)
        if( !fasta.exists() ) exit 1, "Fasta file not found: ${params.fasta}"
                              } else {
    exit 1, "No reference genome specified!"
}






custom_runName = params.name
if( !(workflow.runName ==~ /[a-z]+_[a-z]+/) ){
    custom_runName = workflow.runName
}

// Header log info
log.info "=================================================================="
log.info " Elemento-Melnick-Labs-ATACseq: ATAC-Seq Best Practice v${version}"
log.info "==================================================================="
def summary = [:]
summary['Run Name']     = custom_runName ?: workflow.runName
       //summary['Reads']        = params.reads
summary['Genome']       = params.genome
if(params.bwa_index)  summary['BWA Index'] = params.bwa_index
else if(params.fasta) summary['Fasta Ref'] = params.fasta
summary['Current home']   = "$HOME"
summary['Current user']   = "$USER"
summary['Current path']   = "$PWD"
summary['Working dir']    = workflow.workDir
summary['Output dir']     = params.outdir
summary['Script dir']     = workflow.projectDir
summary['Save Reference'] = params.saveReference
summary['Save Trimmed']   = params.saveTrimmed
summary['Save Intermeds'] = params.saveAlignedIntermediates
if(params.email) summary['E-mail Address'] = params.email
if(workflow.commitId) summary['Pipeline Commit']= workflow.commitId
log.info summary.collect { k,v -> "${k.padRight(15)}: $v" }.join("\n")
log.info "===================================="

index = file(params.index)

       //bwaref = file(params.ref)
results_path = file(params.outdir)
picardconf = file(params.picardconfig)
blacklist = file(params.blacklist)
bcellrefpeaks = file(params.bcellrefpeak)
dnase = file(params.DNASE)
tssenrich = file(params.TSS_ENRICH)
prom = file(params.PROM)
enh = file(params.ENH)
reg2map = file(params.REG2MAP)
reg2mapbed = file(params.REG2MAP_BED)
roadmapmeta = file(params.ROADMAP_META)
ref = file(params.REF)
blackqc = file(params.black)
black = file(params.black)
encodedhs = file(params.encodedhs)
chrsz = file(params.chrsz)
species = params.species
genome = params.genome

if (params.bt2_index){
    lastPath = params.bt2_index.lastIndexOf(File.separator)
    bt2_dir =  params.bt2_index.substring(0,lastPath+1)
    bt2_base = params.bt2_index.substring(lastPath+1)
    ch_bt2_index = Channel
        .fromPath(bt2_dir, checkIfExists: true)
        .ifEmpty { exit 1, "BT2 index directory not found: ${bt2_dir}" }
}



 /*
 * PREPROCESSING - Build BWA index
 */
if(!params.bwa_index && fasta){
    process makeBWAindex {
        tag fasta
        publishDir path: { params.saveReference ? "${params.outdir}/reference_genome" : params.outdir },
                   saveAs: { params.saveReference ? it : null }, mode: 'copy'

        input:
        file fasta from fasta

        output:
        file "BWAIndex" into bwa_index

        script:
        """
        spack load bwa
        mkdir BWAIndex
        bwa index -a bwtsw $fasta
        """
    }
}



/*
 * PREPROCESSING - Build Bt2 index
 */
if(!params.bt2_index && fasta){
    process makeBT2index {
        tag fasta
        publishDir path: { params.saveReference ? "${params.outdir}/reference_genome" : params.outdir },
        saveAs: { params.saveReference ? it : null }, mode: 'copy'

        input:
        file fasta from fasta

        output:
        file "BWAIndex" into bwa_index

        script:
        """
        spack load bowtie2
        mkdir BT2Index
        bowtie2-build $fasta genome
        """
    }
}

////// Check input parameters //////

if (!params.index) {
  exit 1, "Please specify the input table file"
}


sizefactors = Channel.from(1)





fastq = Channel
.from(index.readLines())
.map { line ->
       def list = line.split(',')
       def Sample = list[0]
       def path = file(list[1])
       //def reads = file("$path/*_R{1,2}_001.fastq.gz")
       def reads = file("$path/*_R{1,2}.fastq.gz")
       // def readsp = "$path/*{R1,R2}.trim.fastq.gz"
       //  def R1 = file(list[2])
       //    def R2 = file(list[3])
       def message = '[INFO] '
       log.info message
       [ Sample, path, reads ]
}



/*
 * STEP 2 - NGmerge read trimming
 */
//if(params.notrim){
///    trimmed_reads = read_files_trimming
//} else {
process ngtrim {
    tag "$Sample"
    publishDir "$results_path/$Sample/$Sample", mode: 'copy'

    cpus 6
    executor 'slurm'
        ////clusterOptions '-l h_vmem=2G -l h_rt=24:00:00 -l athena=true'
        //scratch true
    time '8h'
    queue 'panda_physbio'
    memory '12 GB'

    input:
    set Sample, file(path), file(reads) from fastq

    output:
        set Sample, file('*_{1,2}.fastq.gz') into trimmed_reads
        //file '*trimming_report.txt' into trimgalore_results
        //file "*_fastqc.{zip,html}" into trimgalore_fastqc_reports

    script:
        def R1 = reads[0]
        def R2 = reads[1]
        """
        NGmerge -n 4 -z -u 41 -a -1 ${R1} -2 ${R2} -o ${Sample}
        """
            }
//}






process bt2 {
    tag "$Sample"
        publishDir "$results_path/$Sample/$Sample", mode: 'copy'
        //conda 'bowtie2 samtools'

        cpus 8
        executor 'slurm'
        memory '32 GB'
        time '18h'
        queue 'panda_physbio'
        scratch true
        //penv 'smp'
        clusterOptions '--mem-per-cpu=4G --export=ALL'

        input:
        set Sample, file(reads) from trimmed_reads
        file index from ch_bt2_index.collect()
        //file bwaref from bwa_index.collect()
        //file(bwaref) from bwaref

        output:
        set Sample, file("${Sample}.bam") into newbam, genrichbam
        //set Sample, file("${Sample}.bam") into genrichbam
        set Sample, file("${Sample}.bt2.log") into bt2log
   

        script:
        def R1 = reads[0]
        def R2 = reads[1]
        """
        set -o pipefail
        ##spack load bowtie2@2.3.4.1
        bowtie2 -X2000 -x ${index}/genome --local -p 7 --mm -k 4 -1 ${R1} -2 ${R2} 2> ${Sample}.bt2.log | samtools view -bS -q 30 - > ${Sample}.bam
        """
        }


process genrich {
    tag "$Sample"
    publishDir "$results_path/$Sample/$Sample", mode: 'copy'

    executor 'slurm'
    cpus 4
    queue 'panda_physbio'
    time '18h'
    memory '24 GB'
    //penv 'smp'
    //clusterOptions '-l h_vmem=4G -l h_rt=16:00:00 -l athena=true'
    // cpus 8


    input:
    set Sample, file(nbam) from genrichbam
    file black

    output:
    set Sample, file("${Sample}.genrich.narrowPeak") into genrichPeak
    set Sample, file("${Sample}.genrich.log") into genrichLog

    script:
    """
    set -o pipefail
    ##. ~/.spackloads.sh
    samtools sort -@ ${task.cpus} -n -o ${Sample}.nsorted.bam ${nbam}
    Genrich -j -y -r -e chrM,chrY -t ${Sample}.nsorted.bam -o ${Sample}.genrich.narrowPeak -E ${black} -f ${Sample}.genrich.log
    """
}


process processbam {
    tag "$Sample"
    publishDir "$results_path/$Sample/$Sample", mode: 'copy'

    executor 'local'
    cpus 8
    //time '18h'
    //queue 'panda_physbio'
    memory '24 GB'
    //penv 'smp'
    //clusterOptions '-l h_vmem=4G -l h_rt=16:00:00 -l athena=true'
    // cpus 8


    input:
    set Sample, file(nbam) from newbam
    file black

    output:
    set Sample, file("${Sample}.sorted.bam") into sortedbam, sortbamqc, sortedbamqc
    //set Sample, file("${Sample}.sorted.bam") into sortbamqc
    //set Sample, file("${Sample}.sorted.bam") into sortedbamqc
    set Sample, file("${Sample}.sorted.nodup.noM.black.bam") into finalbam, finalbamforqc, bamforsignal
    //set Sample, file("${Sample}.sorted.nodup.noM.black.bam") into finalbamforqc
   // set Sample, file("${Sample}.sorted.nodup.noM.black.bam") into bamforsignal
    set Sample, file("${Sample}*.pbc.qc") into pbcqc
    set Sample, file("${Sample}*.dup.qc") into dupqc
    file("*nsort.fixmate.bam") into fixmatebam
        // file("*window500.hist_data") into hist_data
    file("*window500.hist_graph.pdf") into fragsizes
    set Sample, file("${Sample}.nsorted.nodup.noM.bam") into nsortedbam, nsortedbamforqc
        // set Sample, file("${Sample}.sorted.nodup.noM.black.bam"), file("${Sample}.sorted.nodup.noM.black.bam.bai") into bamforsignal
    //set Sample, file("${Sample}.nsorted.nodup.noM.bam") into nsortedbamforqc

    script:
    """
    #!/bin/bash
    set -o pipefail
    ##. ~/.spackloads.sh
    ##source activate atacFlow
    processAlignment.nf.sh ${nbam} ${black} 8
    """
}


//hist_data.subscribe { println "Received: " + file(hist_data)}

//fragsizes.subscribe { println "Received: " + file(fragsizes)}



process bam2bed {
    tag "$Sample"
    publishDir  "$results_path/$Sample/$Sample", mode: 'copy'

   executor 'slurm'
   cpus 1
   time '18h'
   queue 'panda_physbio'
   memory '12 GB'
   //penv 'smp'
   //clusterOptions '-l h_vmem=4G -l h_rt=16:00:00 -l athena=true'
        // cpus 8
    input:
    set Sample, file(nsbam) from nsortedbam

    output:
    set Sample, file("${Sample}.nodup.tn5.tagAlign.gz") into finalbedqc, finalbed
    //set Sample, file("${Sample}.nodup.tn5.tagAlign.gz") into finalbed
    set Sample, file("${Sample}.nodup.bedpe.gz") into finalbedpe
    set Sample, file("${Sample}.nodup.tn5.tagAlign.gz"), file("${Sample}.nodup.bedpe.gz") into finalbedmacs

    script:
    """
    samtools fixmate ${nsbam} ${Sample}.nsorted.fixmate.nodup.noM.bam
    convertBAMtoBED.sh ${Sample}.nsorted.fixmate.nodup.noM.bam
    cp ${Sample}.nsorted.fixmate.nodup.noM.tn5.tagAlign.gz  ${Sample}.nodup.tn5.tagAlign.gz
    cp ${Sample}.nsorted.fixmate.nodup.noM.bedpe.gz ${Sample}.nodup.bedpe.gz
    """
        }




process callpeaks {
    tag "$Sample"
    publishDir  "$results_path/$Sample/$Sample", mode: 'copy'

    executor 'slurm'
    cpus 1
    queue 'panda_physbio'
    time '8h'
    memory '12 GB'
    //penv 'smp'
    //clusterOptions '-l h_vmem=4G -l h_rt=16:00:00 -l athena=true'
    input:
    set Sample, file(rbed), file(rbedpe) from finalbedmacs
    val sp from species

    output:

    set Sample, file("${Sample}*.narrowPeak") into narrowpeakfile
    set Sample, file("${Sample}.tn5.narrowPeak.gz") into narrowpeak
    set Sample, file("${Sample}.tag.narrow_summits.bed") into summits
    set Sample, file("${Sample}.tn5.broadPeak.gz") into broadpeak
    set Sample, file("${Sample}.tn5.broadPeak.gz") into broadpeakqc
        // set Sample, file("${Sample}/pseudoreps/${Sample}.tn5.pooled.pf.pval0.1.500K.naive_overlap.narrowPeak.gz") into pooledpeaks

    script:
    """
    #!/bin/bash -l
    conda activate idp2
    callbedpepeaks.sh ${rbed} ${Sample} ${sp}
    conda deactivate

    """
        }


process signalTrack {
    tag "$Sample"

    publishDir "$results_path/$Sample/$Sample", mode: 'copy'

    conda 'bioconda::deeptools=3.3.0'
    executor 'slurm'
    queue 'panda_physbio'
    //penv 'smp'
    memory { 8.GB * task.attempt }
    //clusterOptions '-l h_rt=48:00:00 -l athena=true'
    cpus 8
    time '20h'
    errorStrategy { task.exitStatus == 140 ? 'retry' : 'terminate' }

    input:
    set Sample, file(sbam) from bamforsignal
        //val sz from sizefactors


    output:
    set Sample, file("${Sample}.ins.bw") into insertionTrackbw

    script:
    """

    getbamcov.sh ${sbam} ${Sample} ${task.cpus}

    """
    }


finalbedpe.mix(broadpeak)
    .groupTuple(sort: true)
    .set{ fripin }

process frip {
    tag "$Sample"

    publishDir "$results_path/$Sample/frip", mode: 'copy'

    executor 'slurm'
    cpus 1
    queue 'panda_physbio'
    time '8h'
    memory '12 GB'
   //penv 'smp'
   //clusterOptions '-l h_vmem=4G -l h_rt=16:00:00 -l athena=true'

    input:
    set Sample, file(file_list) from fripin
        //set Sample, file(peaks) from broadpeak
        //   file(lncapref) from lncaprefpeaks
    file(bcellref) from bcellrefpeaks
    file(encodedhs) from encodedhs
    file(chrsz) from chrsz

    output:
        //    set Sample, file("${Sample}.bcellref.frip.txt") into frips2
    set Sample, file("${Sample}.frip.qc.txt") into frips

    script:
    """
    #!/bin/bash -l

    ##source activate atacFlow
    ##source ~/miniconda3/etc/profile.d/conda.sh
    ##conda activate atacFlow

    encode_frip.py --chrsz ${chrsz} ${encodedhs} ${Sample}.nodup.bedpe.gz 
    cp *.frip.qc ${Sample}.frip.qc.txt
    """
}





process picardqc {
    tag "$Sample"
    publishDir "$results_path/$Sample/qc", mode: 'copy'

    executor 'slurm'
    cpus 1
    time '8h'
    queue 'panda_physbio'
    memory '12 GB'
    //penv 'smp'
    //clusterOptions '-l h_vmem=4G -l h_rt=16:00:00 -l athena=true'
    input:
    set Sample, file(sortbam) from sortedbamqc
    file(picardconfig) from picardconf 

    output:
    set Sample, file("QCmetrics/${Sample}.picardcomplexity.qc") into picardcomplexity
        //set Sample, file(sortbamqc) into sortbamqc

    script:
    """
    mkdir -p QCmetrics
    java -Xms500m -Xmx5g -jar /home/asd2007/Tools/picard/build/libs/picard.jar EstimateLibraryComplexity I=${sortbam} O=${Sample}.EstimateLibraryComplexity.log
    cp *.EstimateLibraryComplexity.log QCmetrics/${Sample}.picardcomplexity.qc
    """

}


finalbamforqc.mix(nsortedbamforqc)
    .mix(broadpeakqc)
    .mix(finalbedqc)
    .mix(sortbamqc)
    .mix(insertionTrackbw)
    .mix(picardcomplexity)
    .mix(pbcqc)
    .mix(dupqc)
    .mix(frips)
    .mix(bt2log)
    .groupTuple(sort: true)
    .view()
    .set{ qcin }


process atacqc {
    tag "$Sample"

    publishDir "$results_path/$Sample/qc", mode: 'copy'
        //conda 'bds_atac_requirements.txt'

    executor 'slurm'
    cpus 4
    time '32h'
    queue 'panda_physbio'
    memory '32 GB'
    //  scratch true // set in config

    input:
    set Sample, file(file_list) from qcin
    file(dnase) from dnase
    file(tssenrich) from tssenrich
    file(prom) from prom
    file(enh) from enh
    file(reg2map) from reg2map
    file(roadmapmeta) from roadmapmeta
    file(ref) from ref
    file(black) from blackqc
    file(reg2mapbed) from reg2mapbed
    val genome

    output:
    set Sample, file("${Sample}*.preseq.log"), file("${Sample}*_qc.txt"), file("${Sample}*large_vplot.pdf"), file("${Sample}*vplot.pdf"), file("${Sample}_qc.trad.txt"), file("${Sample}*qc.html"), file("*qc.save") into qcdat
    set Sample, file("*.log"), file("*qc") into logs


    script:
    """
    #!/bin/bash -l

    OUTPREFIX=${Sample}
    INPREFIX=${Sample}
    SAMPLE=${Sample}
    PBC=${Sample}.pbc.qc
    echo ${Sample} ${file_list}
    ##spack load jdk

    samtools index -@4 ${Sample}.sorted.nodup.noM.black.bam
    samtools index -@4 ${Sample}.sorted.bam

    source /home/asd2007/miniconda3/etc/profile.d/conda.sh
    conda activate atacFlow && ${baseDir}/bin/run_ataqc.athena.py --workdir \$PWD  \\
    --outdir \$PWD \\
    --outprefix ${Sample} \\
    --genome ${genome} \\
    --ref ${ref} --tss ${tssenrich} \\
    --dnase ${dnase} \\
    --blacklist ${black} \\
    --prom ${prom} \\
    --enh ${enh} \\
    --reg2map ${reg2map} \\
    --reg2map_bed ${reg2mapbed} \\
    --meta ${roadmapmeta} \\
    --alignedbam ${Sample}.sorted.bam  \\
    --alignmentlog ${Sample}.align.log \\
    --coordsortbam ${Sample}.sorted.bam \\
    --duplog ${Sample}.dup.qc \\
    --pbc ${Sample}.pbc.qc \\
    --finalbam ${Sample}.sorted.nodup.noM.black.bam \\
    --finalbed ${Sample}.nodup.tn5.tagAlign.gz \\
    --bigwig ${Sample}.ins.bw \\
    --peaks ${Sample}.tn5.broadPeak.gz \\
    --naive_overlap_peaks ${Sample}.tn5.broadPeak.gz \\
    --idr_peaks ${Sample}.tn5.broadPeak.gz  --processes ${task.cpus}

    """
}
 










workflow.onComplete {
    println ( workflow.success ? "Done!" : "Oops .. something went wrong" )
    def subject = 'pipeline execution'
        def recipient = 'ashley.doane@gmail.com'

    ['mail', '-s', subject, recipient].execute() << """

    Pipeline execution summary
    ---------------------------
    Completed at: ${workflow.complete}
    Duration    : ${workflow.duration}
    Success     : ${workflow.success}
    workDir     : ${workflow.workDir}
    exit status : ${workflow.exitStatus}
    Error report: ${workflow.errorReport ?: '-'}
    """
}



/*
 * Completion e-mail notification
 *
 *workflow.onComplete {
 *
 *    // Set up the e-mail variables
 *    def subject = "[OElab-ATACseq] Successful: $workflow.runName"
 *    if(!workflow.success){
 *      subject = "[OElab-ATACseq] FAILED: $workflow.runName"
 *    }
 *    def email_fields = [:]
 *    email_fields['version'] = version
 *    email_fields['runName'] = custom_runName ?: workflow.runName
 *    email_fields['success'] = workflow.success
 *    email_fields['dateComplete'] = workflow.complete
 *    email_fields['duration'] = workflow.duration
 *    email_fields['exitStatus'] = workflow.exitStatus
 *    email_fields['errorMessage'] = (workflow.errorMessage ?: 'None')
 *    email_fields['errorReport'] = (workflow.errorReport ?: 'None')
 *    email_fields['commandLine'] = workflow.commandLine
 *    email_fields['projectDir'] = workflow.projectDir
 *    email_fields['summary'] = summary
 *    email_fields['summary']['Date Started'] = workflow.start
 *    email_fields['summary']['Date Completed'] = workflow.complete
 *    email_fields['summary']['Nextflow Version'] = workflow.nextflow.version
 *    email_fields['summary']['Nextflow Build'] = workflow.nextflow.build
 *    email_fields['summary']['Nextflow Compile Timestamp'] = workflow.nextflow.timestamp
 *    email_fields['summary']['Pipeline script file path'] = workflow.scriptFile
 *    email_fields['summary']['Pipeline script hash ID'] = workflow.scriptId
 *    if(workflow.repository) email_fields['summary']['Pipeline repository Git URL'] = workflow.repository
 *    if(workflow.commitId) email_fields['summary']['Pipeline repository Git Commit'] = workflow.commitId
 *    if(workflow.revision) email_fields['summary']['Pipeline Git branch/tag'] = workflow.revision
 *    if(workflow.container) email_fields['summary']['Singularity image'] = workflow.container
 *
 *    // Render the TXT template
 *    def engine = new groovy.text.GStringTemplateEngine()
 *    def tf = new File("$baseDir/assets/email_template.txt")
 *    def txt_template = engine.createTemplate(tf).make(email_fields)
 *    def email_txt = txt_template.toString()
 *
 *    // Render the HTML template
 *    def hf = new File("$baseDir/assets/email_template.html")
 *    def html_template = engine.createTemplate(hf).make(email_fields)
 *    def email_html = html_template.toString()
 *
 *    // Render the sendmail template
 *    def smail_fields = [ email: params.email, subject: subject, email_txt: email_txt, email_html: email_html, baseDir: "$baseDir" ]
 *    def sf = new File("$baseDir/assets/sendmail_template.txt")
 *    def sendmail_template = engine.createTemplate(sf).make(smail_fields)
 *    def sendmail_html = sendmail_template.toString()
 *
 *    // Send the HTML e-mail
 *    if (params.email) {
 *        try {
 *          // Try to send HTML e-mail using sendmail
 *          [ 'sendmail', '-t' ].execute() << sendmail_html
 *          log.debug "[NGI-ChIPseq] Sent summary e-mail using sendmail"
 *        } catch (all) {
 *          // Catch failures and try with plaintext
 *          [ 'mail', '-s', subject, params.email ].execute() << email_txt
 *          log.debug "[OElab-ATACseq] Sendmail failed, failing back to sending summary e-mail using mail"
 *        }
 *        log.info "[OElab-ATACseq] Sent summary e-mail to $params.email"
 *    }
 *
 *    // Write summary e-mail HTML to a file
 *    def output_d = new File( "${params.outdir}/Documentation/" )
 *    if( !output_d.exists() ) {
 *      output_d.mkdirs()
 *    }
 *    def output_hf = new File( output_d, "pipeline_report.html" )
 *    output_hf.withWriter { w -> w << email_html }
 *    def output_tf = new File( output_d, "pipeline_report.txt" )
 *    output_tf.withWriter { w -> w << email_txt }
 *
 *    log.info "[OElab-ATACseq] Pipeline Complete"
 *}
 */