Nanopore Guppy Basecalling Assembly with ONT Workflow

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nanopore-guppy-basecalling-assembly-workflow — View Workflow

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Workflow for sequencing with ONT Nanopore, from basecalling to assembly.

Guppy (basecalling of raw reads)
MinIONQC (quality check)
FASTQ merging from multi into one file
Kraken2 (taxonomic classification)
Krona (classification visualization)
Flye (de novo assembly)
Medaka (assembly polishing)
QUAST (assembly quality reports)

Code Snippets

baseCommand: [gzip, -c]

arguments:
  - valueFrom: $(inputs.infile)

CWL From line 7 of bash/compress.cwl

baseCommand: [pigz, -c]

arguments:
  - valueFrom: $(inputs.inputfile)

CWL From line 7 of bash/pigz.cwl

- entryname: script.sh
  entry: |-
    #!/bin/bash
    source /root/miniconda/bin/activate
    conda init bash
    conda activate /unlock/infrastructure/conda/busco_v5.2.2
    busco $@
    # always exit 0 when failed to find genes.
    exit 0

CWL From line 20 of busco/busco.cwl

- entryname: script.sh
  entry: |-
    #!/bin/bash
    source /root/miniconda/bin/activate
    conda init bash
    conda activate /unlock/infrastructure/conda/gtdbtk_v1.7.0
    gtdbtk classify_wf $@

CWL gtdbtk From line 21 of gtdbtk/gtdbtk_classify_wf.cwl

- entryname: nanopore_reads.txt
  entry: |-
    ${
      // let content = "";
      // if (inputs.fast5_files == null)
      //   return content;
      // for (var i = 0; i < inputs.fast5_files.length; i++) {
      //   content += inputs.fast5_files[i].path + "\n"
      // }
      // return content;
      let content = "";
      if (inputs.fast5_files == null)
        return content;
      for (var i = 0; i < inputs.fast5_files.length; i++) {
        content += inputs.fast5_files[i] + "\n"
      }
      return content;
    }

CWL Nanopore From line 24 of guppy/guppy.cwl

- entryname: script.sh
  entry: |-
    #!/bin/bash
    source /root/miniconda/bin/activate
    conda init bash
    conda activate /unlock/infrastructure/conda/krona_v2.8.1
    ktImportText $@

CWL Krona From line 27 of krona/krona.cwl

- entryname: script.sh
  entry: |-
    #!/bin/bash
    source /root/miniconda/bin/activate
    conda init bash
    conda activate /unlock/infrastructure/conda/medaka
    python3 /unlock/infrastructure/binaries/scripts/medaka/medaka.py $@

CWL Medaka From line 33 of medaka/medaka_py.cwl

baseCommand: [python3, "/unlock/infrastructure/binaries/scripts/metagenomics/assembly_bins_readstats.py"]

CWL From line 41 of metagenomics/assembly_bins_readstats.cwl

- entryname: script.sh
  entry: |-
    #!/bin/bash
    source /root/miniconda/bin/activate
    conda init bash
    conda activate /unlock/infrastructure/conda/checkm_v1.1.3
    checkm lineage_wf $@

CWL CheckM From line 20 of checkm/checkm_lineagewf.cwl

- entryname: script.sh
  entry: |-
    #!/bin/bash
    source /unlock/infrastructure/venv/bin/activate
    metaquast.py $@

CWL From line 28 of metaquast/metaquast.cwl

baseCommand: ["java"]

arguments:
  - "-jar"
  - "-Xmx$(inputs.memory)M"
  - "/unlock/infrastructure/binaries/Pilon/pilon-1.24.jar"
  - valueFrom: $(inputs.identifier)_scaffolds_polished
    prefix: "--output"