example

gistfile1.txt

process cutadapt {
  tag "${sampleid}"
  container 'quay.io/biocontainers/cutadapt:1.18--py36_0'
  publishDir "$params.outdir/cutadapt", mode: 'copy'

  input:
  tuple sampleid, path(read1), path(read2) from ch_samples_cutadapt

  output:
  tuple sampleid, path("${sampleid}_R1.cutadapt.fastq.gz"), path("${sampleid}_R2.cutadapt.fastq.gz") into ( ch_cutadapt_fastqc, ch_cutadapt_star, ch_cutadapt_for_sortmerna )
  path("${sampleid}_cutadapt.txt") into ch_cutadapt_multiqc
  path ("version_cutadapt.txt") into ch_version_cutadapt

  script:
  """
  cutadapt -m 25 -q 20 \
  -a $params.clip_forward_adapter \
  -A $params.clip_reverse_adapter \
  -o ${sampleid}_R1.cutadapt.fastq.gz -p ${sampleid}_R2.cutadapt.fastq.gz \
  --cores $task.cpus \
  $read1 $read2 > ${sampleid}_cutadapt.txt 2>&1
  cutadapt --version | sed 's/^/    <br>cutadapt /' > version_cutadapt.txt
  """
}