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#!/usr/bin/env nextflow
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/*
main.nf
*
* --------------------------------------------------------------------------
* Licensed under MIT (https://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_mkfastq/blob/develop/LICENSE)
* --------------------------------------------------------------------------
*
*/
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//  ########  ####  ######  ######## 
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//  ########   ##  ##       ######   
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// Define input variables
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params.name = "run"
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params.bcl = "${baseDir}/../test_data/simple1/*.tar.gz"
params.designFile = "${baseDir}/../test_data/single1/cellranger-tiny-bcl-simple-1_2_0.csv"
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params.mask = ""
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params.astrocyte = false
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params.outDir = "${baseDir}/output"

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// Define list of files
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tarList = Channel
  .fromPath( params.bcl )
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bclCount = Channel
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  .fromPath( params.bcl )
  .count()
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// Define regular variables
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pipelineVersion = "2.2.0-indev"
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name = params.name
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designLocation = Channel
  .fromPath(params.designFile)
  .ifEmpty { exit 1, "design file not found: ${params.designFile}" }
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mask = params.mask
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outDir = params.outDir
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// Define script files
check_designScript = Channel.fromPath("$baseDir/scripts/check_design.py")
untarBCLScript = Channel.fromPath("$baseDir/scripts/untarBCL.sh")
countDesignScript = Channel.fromPath("$baseDir/scripts/countDesign.sh")
fastqcScript = Channel.fromPath("$baseDir/scripts/fastqc.sh")
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versionsScript = Channel.fromPath("$baseDir/scripts/generate_versions.py")
referencesScript = Channel.fromPath("$baseDir/scripts/generate_references.py")
versions_pythonScript = Channel.fromPath("$baseDir/scripts/versions_python.sh")
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//versions_pigzScript = Channel.fromPath("$baseDir/scripts/versions_pigz.sh")
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versions_cellrangerScript = Channel.fromPath("$baseDir/scripts/versions_cellranger.sh")
versions_bcl2fastqScript = Channel.fromPath("$baseDir/scripts/versions_bcl2fastq.sh")
versions_fastqcScript = Channel.fromPath("$baseDir/scripts/versions_fastqc.sh")

// Define report files
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multiqcConf = Channel.fromPath("${baseDir}/configs/multiqc_config.yaml")
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references = Channel.fromPath("${baseDir}/../docs/references.md")

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/*
 * trackStart: track start of pipeline
 */
params.ci = false
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params.dev = false
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process trackStart {
  script:
  """
  hostname
  ulimit -a
  export https_proxy=\${http_proxy}
 
  curl -H 'Content-Type: application/json' -X PUT -d '{ \
      "sessionId": "${workflow.sessionId}", \
      "pipeline": "cellranger_mkfastq", \
      "pipelineVersion": "${pipelineVersion}", \
      "start": "${workflow.start}", \
      "astrocyte": ${params.astrocyte}, \
      "status": "started", \
      "nextflowVersion": "${workflow.nextflow.version}",
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      "ci": ${params.ci},
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      "dev": ${params.dev}}' \
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  "https://xku43pcwnf.execute-api.us-east-1.amazonaws.com/ProdDeploy/pipeline-tracking"
  """
}


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process checkDesignFile {
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  tag "${name}"
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  module 'python/3.6.1-2-anaconda'
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  input:
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    file check_designScript
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    file versions_pythonScript
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    file designLocation
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  output:
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    file("design.checked.csv") into designPaths
    file("design.checked.csv") into designCount
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    file("version_pipeline.txt") into version_pipeline
    file("version_nextflow.txt") into version_nextflow
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    file("version_python.txt") into version_python
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  script:
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    """
    hostname
    ulimit -a
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    noSpaceDesign=\$(echo "${designLocation}" | tr -d ' ')
    if [[ "\${noSpaceDesign}" != "${designLocation}" ]]; then
      mv "${designLocation}" "\${noSpaceDesign}"
    fi
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    python3 check_design.py -d \${noSpaceDesign}
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    bash versions_python.sh > version_python.txt
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    echo "${workflow.nextflow.version}" > version_nextflow.txt
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    echo "${pipelineVersion}" > version_pipeline.txt
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    """

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}
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/* nextflow workflow manifest version calls that aren't compatible with Asrcocyte
    echo "${workflow.manifest.version}" > version_pipeline.txt
*/
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process untarBCL {  
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  tag "${tar.simpleName}"
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  module 'pigz/2.4'
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  input:
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    file untarBCLScript
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    //file versions_pigzScript
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    each file(tar) from tarList
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  output:
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    file("*[!version_pigz.txt]") into bclPaths mode flatten
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    //file("version_pigz.txt") into version_pigz
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  script:
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    """
    hostname
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    ulimit -u 16384
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    ulimit -a
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    bash untarBCL.sh -t ${tar}
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    #bash versions_pigz.sh > version_pigz.txt
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    """

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}

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process mkfastq {
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  tag "${bcl.simpleName}"
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  publishDir "${outDir}/${task.process}", mode: 'copy', pattern: "{*/outs/**/*.fastq.gz}"
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  queue '128GB,256GB,256GBv1,384GB'
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  module 'cellranger/4.0.0:bcl2fastq/2.19.1'
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  input:
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    file versions_cellrangerScript
    file versions_bcl2fastqScript
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    each file(bcl) from bclPaths.collect()
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    file design from designPaths
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  output:
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    file("fq/${bcl.simpleName}/*.fastq.gz") into fastqPaths
    val "${bcl.simpleName}" into bclName
    file("**/outs/**/*.fastq.gz") into cellrangerCount mode flatten
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    file("**/outs/fastq_path/Stats/*") into bqcPaths
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    file("version_cellranger.txt") into version_cellranger
    file("version_bcl2fastq.txt") into version_bcl2fastq
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  script:
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    """
    hostname
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    ulimit -u 16384
    ulimit -a
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    cellranger mkfastq --id=mkfastq_${bcl.simpleName} --run=${bcl} --csv=${design} --ignore-dual-index ${mask}
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    mkdir fq
    mkdir "fq/${bcl.simpleName}"
    find . -name "*.fastq.gz" -exec cp {} fq/${bcl.simpleName}/ \\;
    bash versions_cellranger.sh > version_cellranger.txt
    bash versions_bcl2fastq.sh > version_bcl2fastq.txt
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    """

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}
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if (bclCount.value == 1) {
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  process countDesign {
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    tag "${name}"
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    publishDir "${outDir}/${task.process}/${name}", mode: 'copy'
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    input:
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      file countDesignScript
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      file fastqs from cellrangerCount.collect()
      file design from designCount
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    output:
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      file("Cellranger_Count_Design.csv") into CountDesign
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    script:
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      """
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      hostname
      ulimit -a
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      bash countDesign.sh
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      """

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  }
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}

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process fastqc {
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  tag "${bcl}"
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  module 'fastqc/0.11.5:parallel'
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  input:
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    file fastqcScript    
    file versions_fastqcScript
    file(fastq) from fastqPaths
    each bcl from bclName
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  output:
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    file("*fastqc.zip") into fqcPaths mode flatten
    file("version_fastqc.txt") into version_fastqc
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  script:
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    """
    hostname
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    ulimit -u 16384
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    ulimit -a
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    find *.fastq.gz -exec mv {} ${bcl}.{} \\;
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    bash fastqc.sh
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    bash versions_fastqc.sh > version_fastqc.txt
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    """

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}

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process versions {
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  tag "${name}"
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  module 'python/3.6.1-2-anaconda:cellranger/3.1.0:bcl2fastq/2.19.1:fastqc/0.11.5:pandoc/2.7'
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  input:
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  file versionsScript
  file referencesScript
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  file version_pipeline
  file version_nextflow
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  file version_python
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  //file version_pigz
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  file version_cellranger
  file version_bcl2fastq
  file version_fastqc
  file references
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  output:
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    file("*.yaml") into yamlPaths
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  script:
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    """
    hostname
    ulimit -a
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    python3 generate_versions.py -f version_*.txt -o versions
    python3 generate_references.py -r ${references} -o references
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    """

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}

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process multiqc {
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  tag "${name}"
  publishDir "${outDir}/${task.process}/${name}", mode: 'copy', pattern: "{multiqc*}"
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  module 'multiqc/1.7'
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  input:
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    file multiqcConf
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    file bqc name "bqc/?/*" from bqcPaths.collect()
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    file fqc name "fqc/?/*" from fqcPaths.collect()
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    file yamlPaths
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  output:
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    file("multiqc_report.html") into mqcPaths
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  script:
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    """
    hostname
    ulimit -a
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    #export LC_ALL=C.UTF-8
    #export LANG=C.UTF-8
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    multiqc -c ${multiqcConf} .
    """

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}