fastq_path = params.fastq_path
bam_path = params.bam_path
vcf_path = params.vcf_path

process fastQC{
    input:
      set val(prefix), file(fastq_file) from fastq_files

    output:
    set file("*.zip"), file("*.html") into fastqc_output

    when: fastq_path

    script:
    """
    fastqc -t ${task.cpus} ${fastq_file}
    """
}

process PicardToolsMarkDuplicates{
    input:
    set val(prefix), file(bam_file) from bam_files1

    output:
    file("${prefix}_marked_dup_metrics.txt") into marked_dup_output

    when: bam_path

    """
    java -Xmx${task.memory.toGiga()}g \
    -jar \$PICARD_HOME \
    MarkDuplicates \
    I=${bam_file} \
    O=${prefix}_duplicates.bam \
    M=${prefix}_marked_dup_metrics.txt
    """
}

process PicardToolsCollectInsertSizeMetrics{
    input:
    set val(prefix), file(bam_file) from bam_files2

    output:
    file("${prefix}_insert_size_metrics.txt") into insert_size_metrics_output

    when: bam_path

    """
    java -Xmx${task.memory.toGiga()}g \
    -jar \$PICARD_HOME \
    CollectInsertSizeMetrics \
    I=${bam_file} \
    O=${prefix}_insert_size_metrics.txt \
    H=${prefix}_insert_size_histogram.pdf
    """
}

process BcfToolsStats{
    input:
    set val(prefix), file(vcf_file) from vcf_files1

    output:
    file("${prefix}_bcftools.stats") into bcftools_stats_output

    when: vcf_path

    script:
    """
    bcftools stats ${vcf_file} > ${prefix}_bcftools.stats
    """
}

process SnpEff {
    input:
    set val(prefix), file(vcf_file) from vcf_files2

    output:
    set file("*.csv"), file("${prefix}_snpeff.vcf") into snpeff_vcf_output

    when: vcf_path

    script:
    """
    java -Xmx${task.memory.toGiga()}g \
    -jar \$SNPEFF_HOME \
    -csvStats ${prefix}.csv \
    GRCh37.75 \
    ${vcf_file} > ${prefix}_snpeff.vcf
    """
}

reportsForMultiQC = Channel.empty()
  .mix(
    bcftools_stats_output,
    fastqc_output,
    gatk_variant_eval_output,
    insert_size_metrics_output,
    marked_dup_output,
    snpeff_vcf_output
  ).collect()

process MultiQC {
  input: file ('') from reportsForMultiQC

output:
  file "*multiqc_report.html"
  file "*multiqc_data"

  script:
  """
  multiqc -f ${results_outdir}
  """
}