Hybrid Metagenomic Assembly, Binning, and GEMs Analysis Workflow

public public 1yr ago Version: Version 1 0 bookmarks
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hybrid-metagenomics-workflow
hybrid-metagenomics-workflow
hybrid-metagenomics-workflow
hybrid-metagenomics-workflow
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Workflow (hybrid) metagenomic assembly and binning + GEMs

Accepts both Illumina and Long reads (ONT/PacBio)

Workflow binnning https://workflowhub.eu/workflows/64?version=11 (optional)

  • Metabat2/MaxBin2/SemiBin
  • DAS Tool
  • CheckM
  • BUSCO
  • GTDB-Tk

Workflow Genome-scale metabolic models https://workflowhub.eu/workflows/372 (optional)

  • CarveMe (GEM generation)
  • MEMOTE (GEM test suite)
  • SMETANA (Species METabolic interaction ANAlysis)

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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baseCommand: [ busco ]
CWL BUSCO From line 25 of busco/busco.cwl 
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baseCommand: [ carve ]
CWL carve From line 26 of carveme/carveme.cwl 
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- entryname: script.sh
  entry: |-
    #!/bin/bash
    identifier=$1
    shift;
    echo "Model Mets Reactions Genes" > $identifier\_CarveMe_GEMstats.tsv
    for file in "$@"
    do
      bash /unlock/infrastructure/scripts/GEMstats.sh $file
    done >> $identifier\_CarveMe_GEMstats.tsv
CWL From line 20 of carveme/GEMstats.cwl 
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- entryname: script.sh
  entry: |-
    # !/bin/bash
    export CHECKM_DATA_PATH=/venv/checkm_data
    checkm lineage_wf $@
CWL CheckM From line 34 of checkm/checkm_lineagewf.cwl 
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baseCommand: [ DAS_Tool ]
CWL DAS From line 22 of das_tool/das_tool.cwl 
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baseCommand: [ "Fasta_to_Contig2Bin.sh" ]
CWL From line 22 of das_tool/fasta_to_contig2bin.cwl 
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baseCommand: [ EukRep ]
CWL eukrep From line 22 of eukrep/eukrep.cwl 
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- entryname: script.sh
  entry: |-
    #!/bin/bash
    export GTDBTK_DATA_PATH=$1
    shift;
    gtdbtk classify_wf $@
CWL gtdbtk From line 18 of gtdbtk/gtdbtk_classify_wf.cwl 
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baseCommand: [ "run_MaxBin.pl" ]
CWL SqueezeMeta From line 22 of maxbin2/maxbin2.cwl 
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baseCommand: [ memote ]
CWL memote From line 22 of memote/memote.cwl 
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baseCommand: [aggregateBinDepths.pl]
CWL From line 22 of metabat2/aggregateBinDepths.cwl 
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baseCommand: [ metabat2 ]

arguments:
  - prefix: "--outFile"
    valueFrom: MetaBAT2_bins/$(inputs.identifier)_MetaBAT2_bin
CWL MetaBAT 2 From line 23 of metabat2/metabat2.cwl 
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baseCommand: [jgi_summarize_bam_contig_depths]

arguments:
  - position: 1
    prefix: '--outputDepth'
    valueFrom:  $(inputs.identifier)_contigDepths.tsv
CWL From line 23 of metabat2/metabatContigDepths.cwl 
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baseCommand: ["python3", "/scripts/metagenomics/assembly_bins_readstats.py"]
CWL From line 38 of metagenomics/assembly_bins_readstats.cwl 
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baseCommand: ["python3", "/scripts/metagenomics/bins_summary.py"]
CWL From line 41 of metagenomics/bins_summary.cwl 
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baseCommand: [ prodigal ]

arguments:
  # - valueFrom: "sco" # What is the sco format?
  #   prefix: "-f"
  - valueFrom: $(inputs.input_fasta.nameroot).prodigal
    prefix: "-o"
  - valueFrom: $(inputs.input_fasta.nameroot).prodigal.ffn
    prefix: "-d"
  - valueFrom: $(inputs.input_fasta.nameroot).prodigal.faa
    prefix: "-a"
CWL prodigal From line 18 of prodigal/prodigal.cwl 
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baseCommand: [ SemiBin, single_easy_bin ]
CWL From line 24 of semibin/semibin_single_easy_bin.cwl 
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baseCommand: [ smetana ]
CWL smetana From line 24 of smetana/smetana.cwl 
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baseCommand: [ raw_n50 ]
CWL n50 calculator From line 12 of stats/raw_n50.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_metagenomics_assembly.cwl
Name: hybrid-metagenomics-workflow
Version: Version 1
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Copyright: Public Domain
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