bbduk_nf.config

#! /usr/bin/env nextflow

samples_ch = Channel.fromPath("fastqs/*.fastq")

process FASTQS {
   
  input: 
    file reads from samples_ch
  output:
    file 'fastqc_logs' into fastqc_ch
  
  script:
  """
  mkdir xx
  xxx
  """
}

process align_sample {

  input:
  file 'reference.fa' from genome_ch
  file 'sample.fq' from reads_ch

  output:
  file 'sample.bam' into bam_ch

  script:
  """
  bwa mem reference.fa sample.fq \
        | samtools sort -o sample.bam
  """
}

process index_sample {

  input:
  file 'sample.bam' from bam_ch
  
  output:
  file 'sample.bai' into bai_ch

  script:
  """
  samtools index sample.bam
  """
}