baseCommand: [pigz, -c]

arguments:
  - valueFrom: $(inputs.inputfile)

baseCommand: [bbmap.sh]

arguments:
  - "-Xmx$(inputs.memory)M"
  - "printunmappedcount"
  - "overwrite=true"
  - "bloom=t"
  - "statsfile=$(inputs.identifier)_BBMap_stats.txt"
  - "covstats=$(inputs.identifier)_BBMap_covstats.txt"
  - |
    ${
      if (inputs.output_mapped){
        return 'outm1='+inputs.identifier+'_filtered_1.fq.gz \
                outm2='+inputs.identifier+'_filtered_2.fq.gz';
      } else {
        return 'outu1='+inputs.identifier+'_filtered_1.fq.gz \
                outu2='+inputs.identifier+'_filtered_2.fq.gz';
      }
    }
  # - "fast"
  # - "minratio=0.9"
  # - "maxindel=3"
  # - "bwr=0.16"
  # - "bw=12"
  # - "minhits=2"
  # - "qtrim=r"
  # - "trimq=10"
  # - "untrim"
  # - "idtag"
  # - "kfilter=25"
  # - "maxsites=1"
  # - "k=14"
  # - "nodisk=t"
  # - "out=$(inputs.identifier)_BBMap.sam"
  # - "rpkm=$(inputs.identifier).rpkm"

- entryname: script.sh
  entry: |-
    #!/bin/bash
    echo -e "\
    #/usr/bin/python3
    import sys\n\
    headers = set()\n\
    c = 0\n\
    for line in sys.stdin:\n\
      splitline = line.split()\n\
      if line[0] == '>':    \n\
        if splitline[0] in headers:\n\
          c += 1\n\
          print(splitline[0]+'.x'+str(c)+' '+' '.join(splitline[1:]))\n\
        else:\n\
          print(line.strip())\n\
        headers.add(splitline[0])\n\
      else:\n\
        print(line.strip())" > ./dup.py
    out_name=$1
    shift

    if file $@ | grep gzip; then
      zcat $@ | python3 ./dup.py | gzip > $out_name
    else
      cat $@ | python3 ./dup.py | gzip > $out_name
    fi