main.nf

#!/usr/bin/env nextflow

// Path to an input file, or a pattern for multiple inputs
// Note - $baseDir is the location of this workflow file main.nf


// Define Input variables
params.name = "run"
params.bcl = "${baseDir}/../test_data/*.tar.gz"
params.designFile = "${baseDir}/../test_data/design.csv"
params.outDir = "${baseDir}/output"
params.multiqcConf = "${baseDir}/conf/multiqc_config.yaml"
params.references = "${baseDir}/../docs/references.md"


// Define List of Files
tarList = Channel
  .fromPath( params.bcl )
bclCount = Channel
  .fromPath( params.bcl )
  .count()


// Define regular variables
name = params.name
designLocation = Channel
  .fromPath(params.designFile)
  .ifEmpty { exit 1, "design file not found: ${params.designFile}" }
outDir = params.outDir
multiqcConf = params.multiqcConf
references = params.references


process checkDesignFile {

  tag "${name}"
  publishDir "${outDir}/misc/${task.process}/${name}", mode: 'copy'
  module 'python/3.6.1-2-anaconda'

  input:
    file designLocation

  output:
    file("design.checked.csv") into designPaths
    file("design.checked.csv") into designCount

  script:
    """
    hostname
    ulimit -a
    python3 ${baseDir}/scripts/check_design.py -d ${designLocation}
    """

}


process untarBCL {

  tag "${tar}"
  publishDir "${outDir}/${task.process}", mode: 'copy'
  module 'pigz/2.4'

  input:
    file tar from tarList

  output:
    file("*") into bclPaths mode flatten

  script:
    """
    hostname
    ulimit -a
    bash ${baseDir}/scripts/untarBCL.sh -t ${tar}
    """

}


process mkfastq {

  tag "${bcl.baseName}"
  queue '128GB,256GB,256GBv1,384GB'
  publishDir "${outDir}/${task.process}", mode: 'copy', pattern: "{*/outs/**/*.fastq.gz}"
  module 'cellranger/3.0.2:bcl2fastq/2.19.1'

  input:
    each bcl from bclPaths.collect()
    file design from designPaths

  output:
    file("**/outs/**/*.fastq.gz") into fastqPaths
    file("**/outs/**/*.fastq.gz") into cellrangerCount
    file("**/outs/fastq_path/Stats/Stats.json") into bqcPaths
    val "${bcl.baseName}" into bclName

  script:
    """
    hostname
    ulimit -a  
    cellranger mkfastq --id=${bcl.baseName} --run=${bcl} --csv=${design} -r \$SLURM_CPUS_ON_NODE  -p \$SLURM_CPUS_ON_NODE  -w \$SLURM_CPUS_ON_NODE 
    """

}


if (bclCount.value == 1) {

  process countDesign {

    tag "${name}"
    publishDir "${outDir}/misc/${task.process}/${name}", mode: 'copy'

    input:
      file fastqs from cellrangerCount.collect()
      file design from designCount

    output:
      file("Cellranger_Count_Design.csv") into CountDesign

    script:
      """
      bash ${baseDir}/scripts/countDesign.sh
      """

  }

}


process fastqc {

  tag "${bclName}"
  queue 'super'
  publishDir "${outDir}/misc/${task.process}/${name}/${bclName}", mode: 'copy', pattern: "{*fastqc.zip}"
  module 'fastqc/0.11.5:parallel'

  input:
    file fastqPaths
    val bclName

  output:
    file("*fastqc.zip") into fqcPaths

  script:
    """
    hostname
    ulimit -a
    find *.fastq.gz -exec mv {} ${bclName}.{} \\;
    bash ${baseDir}/scripts/fastqc.sh
    """

}


process versions {

  tag "${name}"
  publishDir "${outDir}/misc/${task.process}/${name}", mode: 'copy'
  module 'python/3.6.1-2-anaconda:cellranger/3.0.2:bcl2fastq/2.19.1:fastqc/0.11.5:pandoc/2.7'

  input:

  output:
    file("*.yaml") into yamlPaths

  script:
    """
    hostname
    ulimit -a
    echo ${workflow.nextflow.version} > version_nextflow.txt
    bash ${baseDir}/scripts/versions_mkfastq.sh
    bash ${baseDir}/scripts/versions_fastqc.sh
    python3 ${baseDir}/scripts/generate_versions.py -f version_*.txt -o versions
    python3 ${baseDir}/scripts/generate_references.py -r ${references} -o references
    """

}


process multiqc {

  tag "${name}"
  queue 'super'
  publishDir "${outDir}/${task.process}/${name}", mode: 'copy', pattern: "{multiqc*}"
  module 'multiqc/1.7'

  input:
    file bqc name "bqc/?/*" from bqcPaths.collect()
    file fqc name "fqc/*" from fqcPaths.collect()
    file yamlPaths

  output:
    file("multiqc_report.html") into mqcPaths

  script:
    """
    hostname
    ulimit -a
    multiqc -c ${multiqcConf} .
    """

}