nextflow-issues

• how to optimize sequential workflow

process with .out.collect() not rerunning if the first process has been run, e.g

promle( data )
integration_plot("${params.project_folder}/${params.output_mle}/", promle.out.collect(), matrices)

• work around using the same process twice within a workflow

for example, this will not work because promle cannot be called twice

if ( 'output_mle' in params.keySet() ) {
  data = channel.fromPath( "${params.project_folder}/${params.output_mle}/*mle.sh" )
  data = data.filter{ ! file( "$it".replace(".mle.sh", ".sgrna_summary.txt") ).exists() }
  promle( data )
      
  if ( 'mle_matrices' in params.keySet() ) {
    data = channel.fromPath( "${params.project_folder}/${params.output_mle}/mle_matrix/*mle.sh" )
    data = data.filter{ ! file( "$it".replace(".mle.sh", ".sgrna_summary.txt") ).exists() }
    promle( data )
    matrices="${params.mle_matrices}"
    integration_plot("${params.project_folder}/${params.output_mle}/mle_matrix/", promle.out.collect(), matrices)
  }
}