Integrated Workflow: Metagenomic Bins to Metabolic Models (GEMs)

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Workflow for Metagenomics from bins to metabolic models (GEMs)

Prodigal gene prediction
CarveMe genome scale metabolic model reconstruction
MEMOTE for metabolic model testing
SMETANA Species METabolic interaction ANAlysis

Code Snippets

baseCommand: [pigz, -c]

arguments:
  - valueFrom: $(inputs.inputfile)

CWL From line 16 of bash/pigz.cwl

baseCommand: [ bbduk.sh ]

CWL BBMap From line 23 of bbmap/bbduk_filter.cwl

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"

CWL BBMap From line 90 of bbmap/bbmap_filter-reads.cwl

- 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

baseCommand: [ busco ]

CWL BUSCO From line 25 of busco/busco.cwl

baseCommand: [ carve ]

CWL carve From line 26 of carveme/carveme.cwl

- 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

- 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

baseCommand: [ DAS_Tool ]

CWL DAS From line 22 of das_tool/das_tool.cwl

baseCommand: [ "Fasta_to_Contig2Bin.sh" ]

CWL From line 22 of das_tool/fasta_to_contig2bin.cwl

baseCommand: [ EukRep ]

CWL eukrep From line 22 of eukrep/eukrep.cwl

baseCommand: [ fastp ]

CWL fastp From line 137 of fastp/fastp.cwl

baseCommand: [ fastqc ]

CWL FastQC From line 6 of fastqc/fastqc.cwl

- 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

baseCommand: [ flye ]

CWL Flye From line 16 of flye/flye.cwl

- 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

baseCommand: [ kraken2 ]

CWL kraken2 From line 6 of kraken2/kraken2.cwl

baseCommand: [ ktImportTaxonomy ]

CWL Krona From line 15 of krona/krona.cwl

baseCommand: [ "run_MaxBin.pl" ]

CWL SqueezeMeta From line 22 of maxbin2/maxbin2.cwl

baseCommand: [ medaka.py ]

CWL Medaka From line 17 of medaka/medaka_consensus_py.cwl

baseCommand: [ memote ]

CWL memote From line 22 of memote/memote.cwl

baseCommand: [aggregateBinDepths.pl]

CWL From line 22 of metabat2/aggregateBinDepths.cwl

baseCommand: [ metabat2 ]

arguments:
  - prefix: "--outFile"
    valueFrom: MetaBAT2_bins/$(inputs.identifier)_MetaBAT2_bin

CWL MetaBAT 2 From line 23 of metabat2/metabat2.cwl

baseCommand: [jgi_summarize_bam_contig_depths]

arguments:
  - position: 1
    prefix: '--outputDepth'
    valueFrom:  $(inputs.identifier)_contigDepths.tsv

CWL From line 23 of metabat2/metabatContigDepths.cwl

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

CWL From line 38 of metagenomics/assembly_bins_readstats.cwl

baseCommand: ["python3", "/scripts/metagenomics/bins_summary.py"]

CWL From line 41 of metagenomics/bins_summary.cwl

- 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

baseCommand: [ NanoPlot ]

CWL NanoPlot From line 27 of nanoplot/nanoplot.cwl

baseCommand: ["java"]

arguments:
  - "-jar"
  - "-Xmx$(inputs.memory)M"
  - "/venv/share/pilon-1.24-0/pilon.jar"
  - valueFrom: $(inputs.identifier)_pilon_polished
    prefix: "--output"

CWL From line 81 of pilon/pilon.cwl

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

baseCommand: [ metaquast.py ]

CWL From line 7 of quast/metaquast.cwl

baseCommand: [ samtools, idxstats ]

CWL From line 44 of samtools/samtools_idxstats.cwl

baseCommand: [ samtools, index ]

arguments:
  - valueFrom: $(inputs.bam_file.basename).bai
    position: 2

CWL From line 39 of samtools/samtools_index.cwl

- entryname: script.sh
  entry: |-
    #!/bin/bash
    samtools view -@ $2 -hu $3 | samtools sort -@ $2 -o $1.sorted.bam

CWL SAMtools From line 17 of samtools/sam_to_sorted-bam.cwl

baseCommand: [ SemiBin, single_easy_bin ]

CWL From line 24 of semibin/semibin_single_easy_bin.cwl

baseCommand: [ smetana ]

CWL smetana From line 24 of smetana/smetana.cwl

- entryname: input_spades.json
  entry: |-
    [
      {
        orientation: "fr",
        type: "paired-end",
        right reads: $( inputs.forward_reads.map( function(x) {return  x.path} ) ),
        left reads: $( inputs.reverse_reads.map( function(x) {return  x.path} ) )
      }            
      ${
        var pacbio=""
          if (inputs.pacbio_reads != null) {
           pacbio+=',{ type: "pacbio", single reads: ["' + inputs.pacbio_reads.map( function(x) {return  x.path} ).join('","') + '"] }' 
        }
        return pacbio;
      }
      ${
        var nanopore=""
          if (inputs.nanopore_reads != null) {
           nanopore+=',{ type: "nanopore", single reads: ["' + inputs.nanopore_reads.map( function(x) {return  x.path} ).join('","') + '"] }'
          //  nanopore+=',{ type: "nanopore", single reads: ["' + inputs.nanopore_reads.join('","') + '"] }'
        }
        return nanopore;
      }
    ]

CWL From line 15 of spades/spades.cwl

baseCommand: [ spades.py, --dataset, input_spades.json ]

arguments:
  - valueFrom: $(runtime.outdir)/output
    prefix: -o
  - valueFrom: $(inputs.memory / 1000)
    prefix: --memory