LongRead Quality Control and Filtering Workflow for Accurate Taxonomic Classification and Enhanced Data Quality

public public 1yr ago Version: Version 1 0 bookmarks
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longread-quality-control-and-filtering
longread-quality-control-and-filtering
longread-quality-control-and-filtering
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Workflow for LongRead Quality Control and Filtering

  • NanoPlot (read quality control) before and after filtering
  • Filtlong (read trimming)
  • Kraken2 taxonomic read classification before and after filtering
  • Minimap2 read filtering based on given references

Code Snippets

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baseCommand: [pigz, -c]

arguments:
  - valueFrom: $(inputs.inputfile)
CWL From line 16 of bash/pigz.cwl 
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- 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
CWL From line 22 of bbmap/prepare_fasta_db.cwl 
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- entryname: script.sh
  entry: |-
    #!/bin/bash
    outname=$1
    longreads=$2
    shift;shift;
    filtlong $longreads $@ 2> >(tee -a $outname.filtlong.log>&2) | gzip > $outname.fastq.gz
CWL Filtlong From line 23 of filtlong/filtlong.cwl 
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baseCommand: [ kraken2 ]
CWL kraken2 From line 6 of kraken2/kraken2.cwl 
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baseCommand: [ ktImportTaxonomy ]
CWL Krona From line 15 of krona/krona.cwl 
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- entryname: script.sh
  entry: |-
    #!/bin/bash
    #   $1 = mapped/unmapped (-F -f)
    # 1 $2 = ref
    # 2 $3 = fastq
    # 3 $4 = preset (map-ont)
    # 4 $5 = threads
    # 5 $6 = identifier

    minimap2 -a -t $5 -x $4 $2 $3 | samtools fastq -@ $5 -n $1 4 | pigz -p $5 > $6_filtered.fastq.gz
CWL SAMtools Minimap2 From line 19 of minimap2/minimap2_to_fastq.cwl 
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baseCommand: [ NanoPlot ]
CWL NanoPlot From line 27 of nanoplot/nanoplot.cwl
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Created: 1yr ago
Updated: 1yr ago
Maitainers: public
URL: https://gitlab.com/m-unlock/cwl/-/blob/master/cwl/workflows/workflow_nanopore_quality.cwl
Name: longread-quality-control-and-filtering
Version: Version 1
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Copyright: Public Domain
License: None
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