Some minimal nextflow examples

input1.fa

>1
CGAT
>2
CGAT

input2.fa

>1
CGAT
>2
CGAT

permanent_file.nextflow

#!/usr/bin/env nextflow

inputFiles = Channel.fromPath("input*.fa")

process myTest {
  input:
  file inputFile from inputFiles
  output:
  file "${inputFile}.out" into outputFiles
  script:
  """
  wc -l ${inputFile} > ${inputFile}.out
  """
}

myStoreDir = "$HOME/tmp/data"
inputFilesStore = Channel.fromPath("${myStoreDir}/input*.fa")

process myTestWithStore {
  storeDir myStoreDir
  input:
  file inputFile from inputFilesStore
  output:
  file "${inputFile}.out" into outputFilesStore
  script:
  """
  wc -l ${inputFile} > ${inputFile}.out
  """
}