Add a new Pipeline to MACSEK

To add a new Pipeline to MACSEK you first f all have to write a nextflow pipeline. The entry files for the Pipline will be present in the same folder as the Pipline start. So the input Channel of the nextflow pipeline must search for the input files in the present directory. The results must be saved also in the present directory in a Folder called 'out/'. In the up coming example we will add a fastqc/multiqc Pipeline to MACSEK. As disribed above write a pipeline with these requirements. The fastqc/multiqc Pipleine would be look like this.

Channel.fromPath('*.fq').set{channel_fastqc_file}

process fastqc{

  publishDir 'out/', mode:'copy'
  cpus 4
  memory '4 GB'
  input:
    file(fastq) from channel_fastqc_file
  output:
    file('*')
    file ('*.zip') into channel_multiqc
  script:
    """
      fastqc $fastq
    """
}

process multiqc{
  publishDir 'out/', mode:'copy'
  cpus 4
  memory '4 GB'
  input:
    file(fastqc_result) from  channel_multiqc
  output:
    file('*')

  script:
    """
      multiqc $fastqc_result
    """
}