Virus genome assembly with Unicycler and Spades.

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Virus genome assembly with Unicycler and Spades, The 2 assemblers works in parallel. The graph visualization is made with Bandage. workflow git repository : https://github.com/fjrmoreews/cwl-workflow-SARS-CoV-2/blob/master/Assembly/workflow/assembly-wf-virus.cwl Based on https://github.com/galaxyproject/SARS-CoV-2/blob/master/genomics/2-Assembly/as_wf.png

Code Snippets

baseCommand: bash

arguments: [bandage_image_launch.sh]

hints:
  DockerRequirement:
    dockerPull: "fjrmore/bandage" 

CWL Bandage From line 72 of tool/bandage-image.cwl

- entryname: bandage_image_launch.sh
  entry: |
         #!/bin/bash
         ###########################
         # Bandage image wrapper  
         export QT_QPA_PLATFORM=minimal
         TMPDIR=$PWD"/tmp_runtime-bandage"
         mkdir -p $TMPDIR
         export XDG_RUNTIME_DIR=$TMPDIR
         GRAPH="$(inputs.graph.path)"
         IMAGE="$(inputs.graph.nameroot).$(inputs.format)"
         Bandage image $GRAPH $IMAGE  \\
         ${
          var opt=""
          if(inputs.height!=null){ 
           opt+=" --height "+inputs.height+ " "
          }
          if(inputs.width!=null){ 
           opt+=" --width "+inputs.width +" "
          }
          if(inputs.node_length==true){ 
           opt+=" --names "
          }
          if(inputs.node_length==true){ 
           opt+=" --lengths "
          }
          return opt
         }  

CWL Bandage From line 85 of tool/bandage-image.cwl

baseCommand: bash

arguments: [bandage_info_launch.sh]

hints:
  DockerRequirement:
    dockerPull: "fjrmore/bandage" 

CWL Bandage From line 46 of tool/bandage-info.cwl

- entryname: bandage_info_launch.sh
  entry: |
         #!/bin/bash
         ###########################
         # Bandage info wrapper  
         export QT_QPA_PLATFORM=minimal
         TMPDIR=$PWD"/tmp_runtime-bandage"
         mkdir -p $TMPDIR
         export XDG_RUNTIME_DIR=$TMPDIR
         Bandage info '$(inputs.graph.path)' \\
         ${
          var opt=""
          if(inputs.tsv==true){ 
           opt+=" --tsv "
          }
          return opt
         } \\
          > assembly_graph_info.txt

CWL Bandage From line 59 of tool/bandage-info.cwl

baseCommand:
  - bash

inputs:
  libraries_metadata:
    type:
      type: array
      items:
          type: record
          fields:
             lib_index: int? 
             orientation: string?
             lib_type: string? 
    doc: |
        reads library metadata
        related to   libraries_fwd_rev and libraries_mono inputs
        lib_index(id) must match
  libraries_fwd_rev:
    type:
      type: array
      items:
          type: record
          fields:
             lib_index: int? 
             fwd_reads: File?
             rev_reads: File?
    doc: |
        reads file
        orientation must be a value in  ff, fr, rf
        K-mer choices can be chosen by SPAdes instead of being entered manually
  libraries_mono:
    type:
      type: array
      items:
          type: record
          fields:
             lib_index: int? 
             file_type: string?
             reads: File?
    doc: |
        reads file
        file_type value must be in : interleaved, merged, unpaired
  pacbio_reads:
    type: File[]?
  nanopore_reads:
    type: File[]?
  sanger_reads:
    type: File[]?
  trusted_contigs:
    type: File[]?
  untrusted_contigs:
    type: File[]?
  auto_kmer_choice:
    type:  boolean
    default: true
    doc: |
        Automatically choose k-mer values.
        K-mer choices can be chosen by SPAdes instead of being entered manually
  kmers:
    type:  string
    default: "21,33,55"
    doc: |
        K-mers to use, separated by commas.
        Comma-separated list of k-mer sizes to be used 
        (all values must be odd, less than 128, listed in ascending order,
         and smaller than the read length). The default value is 21,33,55
  cov_state:
    type:
     - "null"
     -  type: enum
        symbols:
          - off
          - value
          - auto
    doc: |
        Coverage cutoff ( 'auto', or 'off', or 'value'). auto if null
        when cov_state=value (User Specific) , cov_cutoff must be provided
  cov_cutoff:
    type:  float?
    doc: |
        coverage cutoff value (a positive float number )
  iontorrent:
    type:  boolean
    default: false
    doc: |
        true if Libraries are IonTorrent reads.
  sc:
    type:  boolean
    default: false
    doc: |
        This option is required for MDA. 
        true if single-cell data. 
  onlyassembler:
    type: boolean
    default: false
    doc: |
        Run only assembly if true
        (without read error correction)
  careful:
    type: boolean
    default: true
    doc: |
        Careful correction.
        Tries to reduce number of mismatches and short indels. 
        Also runs MismatchCorrector, a post processing tool,
        which uses BWA tool (comes with SPAdes).

outputs:
  out_contig_stats:
    type: File
    outputBinding:
      glob: out_contig_stats.*
    doc: "contig stats, default column_names: name,length,coverage"
  out_scaffold_stats:
    type: File
    outputBinding:
      glob: out_scaffold_stats.*
    doc: "scaffold stats, default column_names: name,length,coverage"

  out_contigs:
    type: File
    outputBinding:
      glob: contigs.fasta
    doc: "contigs (fasta sequence)"

  out_scaffolds:
    type: File
    outputBinding:
      glob: scaffolds.fasta
    doc: "scaffolds (fasta sequence)"
#  - id: all_script
#    type:
#      - type: array
#        items: File
#    outputBinding:
#      glob: "*.sh"  
#    doc: "generated script to run spades. for learning purpose" 
  all_log:
    type:
      - type: array
        items: File
    outputBinding:
      glob: "*.log"  
    doc: "spades output log and warnings" 
#  - id: out_log
#    type: File
#    outputBinding:
#      glob: spades.log
#    doc: "spades output log"
  assembly_graph:
    type: File
    outputBinding:
      glob: assembly_graph.fastg
    doc: "assembly graph" 
  assembly_graph_with_scaffolds:
    type: File
    outputBinding:
      glob: assembly_graph_with_scaffolds.gfa
    doc: "assembly graph with scaffolds" 

arguments:
  - spades_wrapper.sh

CWL From line 5 of tool/spades.cwl

- entryname: write_tsv.py
  entry: |
         #######input file here
         #!/usr/bin/env python
         import sys,re
         search_str = r'^>(NODE|\S+)_(\d+)(?:_|\s)length_(\d+)_cov_(\d+\.*\d*).*\$'
         replace_str = r'\1_\2\t\3\t\4'
         cmd = re.compile(search_str)
         sys.stdout.write('#name\tlength\tcoverage\n')
         for i,line in enumerate(sys.stdin):
            if cmd.match(line):
               sys.stdout.write(cmd.sub(replace_str,line))

CWL From line 171 of tool/spades.cwl

- entryname: spades_wrapper.sh
  entry: |
         ####################spades launcher
         #!/bin/bash
         ## An example command looks like:
         ## spades.py -k 21,33,55,77,99,127 --careful -1 Y.fastq.gz -2 X.fastq.gz -t 24 -o output 
         read -d '' MEMORY_GB << EOF
         ${ 
          //compute memory limits
          var mem="250"
          if(runtime.ram){
            var bt=runtime.ram * 1048576 //mebibytes to bytes               
            bt=bt*0.000000001 //bytes to Gigabytes 
            mem=parseInt(bt)
          }
          return "-"+mem
         }
         EOF
         #echo "MEMORY_GB limit: \$MEMORY_GB"
         read -d '' CORES << EOF
         ${ 
          //compute core / slot
          var cores="16" 
          if(runtime.cores){
            cores=runtime.cores
          }
          return  cores
         }
         EOF
         #echo "CORES : \$CORES"
         read -d '' SPADES_OPT << EOF
         ${   
           var opt=""
             if (inputs.sc==true){
              opt+=" --sc "
             }
             if (inputs.onlyassembler==true){
              opt+=" --only-assembler "
             }
             if (inputs.careful==true){
              opt+=" --careful "
             }
           return opt  
         }
         EOF


         read -d '' CMD_BASE << EOF
         spades.py -o . --disable-gzip-output  
           \$SPADES_OPT 
          -t \$CORES -m \$MEMORY_GB
         ${   
           var opt=""
             if (inputs.auto_kmer_choice==false){
              opt+=" -k "+inputs.kmers 
             }
           return opt  
         }
         ${
           var opt=""
           if (inputs.cov_state==null || inputs.cov_state == "auto"){
                opt+=" --cov-cutoff 'auto' "
            }
           else if (inputs.cov_state == "value"){
                opt+=" --cov-cutoff '"+inputs.cov_cutoff+"' "
            }
           if (inputs.iontorrent==true ){
                opt+=" --iontorrent "
           } 
           return opt  
         }
         EOF
         ##########################################
         ##Sequence files from libraries
         read -d '' CMD_READ1 << EOF
         ${
         var opt=""
         var lib_prefix = {}
         var lib_meta=inputs.libraries_metadata   
         if (lib_meta!=null){
             for(var j=0; j<lib_meta.length;j++){
                var prefix=""
                var lmeta=lib_meta[j]
                if (lmeta.lib_type !=null && lmeta.lib_type == "paired_end"){
                     prefix = 'pe'
                 } 
                else if (lmeta.lib_type !=null && lmeta.lib_type == "mate_paired"){
                     prefix = 'mp'
                 }
                else if (lmeta.lib_type !=null && lmeta.lib_type == "nxmate_paired"){
                     prefix = 'nxmate'
                 }                       
                else {
                     prefix = 'hqmp'
                 }
                var idx=lmeta.lib_index
                lib_prefix[idx]=prefix
                opt+=" --"+prefix+idx+"-"+lmeta.orientation+" "
            } 
          }  
         var libraries = []
         if(inputs.libraries_fwd_rev!=null){ 
            for (var i = 0; i < inputs.libraries_fwd_rev.length ; i++) {
               var lib=inputs.libraries_fwd_rev[i] 
               lib.file_type="separate"
               libraries[i] = lib
            }
          } 
         if(inputs.libraries_mono!=null){
            for (var i = 0; i < inputs.libraries_mono.length ; i++) {
              var ei= libraries.length
              libraries[ei] = inputs.libraries_mono[i]
            }
         }  
         for(var j=0; j<libraries.length;j++){
           var lib=libraries[j]
           var idx=lib.lib_index  
           var prefix=lib_prefix[idx]
           if(lib.file_type!=null){
              if ( lib.file_type == "separate"){
                opt+=" --"+prefix+idx+"-1 "+"fastq:"+lib.fwd_reads.path+" "
                opt+=" --"+prefix+idx+"-2 "+"fastq:"+lib.rev_reads.path+" "
              }else{
                var suffix
                if ( lib.file_type == "interleaved"){
                  suffix="12"
                }
                if ( lib.file_type == "merged"){
                  suffix="m"
                }
                if ( lib.file_type == "unpaired"){
                  suffix="s"
                }
                opt+=" --"+prefix+idx+"-"+suffix+" "+"fastq:"+lib.reads.path+" "
              }
            }
          }  
           return opt  
         }
         EOF
         ##########################################



         #########################>DEBUG

         ##########################################
         ##Sequence files from libraries
         read -d '' ZZDEBUG << EOF
         ${
         //var opt="inputs.libraries_metadata.length:"+inputs.libraries_metadata.length+" "              
         //var str = JSON.stringify(inputs.libraries_metadata)
         var opt=""
         var lib_prefix = {}
         var lib_meta=inputs.libraries_metadata   
         if (lib_meta!=null){
             opt+=" not null "
             for(var j=0; j<lib_meta.length;j++){
                var prefix=""
                var lmeta=lib_meta[j]

                opt+=" !!-AA-"+lmeta.lib_index+"-"+lmeta.orientation+" "
            } 
          }  
         var libraries = []
         if(inputs.libraries_fwd_rev!=null){ 
            for (var i = 0; i < inputs.libraries_fwd_rev.length ; i++) {
               var lib=inputs.libraries_fwd_rev[i] 
               lib.file_type="separate"
               libraries[i] = lib
            }
          } 
         if(inputs.libraries_mono!=null){
            for (var i = 0; i < inputs.libraries_mono.length ; i++) {
              var ei= libraries.length
              libraries[ei] = inputs.libraries_mono[i]
            }
         }  
         for(var j=0; j<libraries.length;j++){
           var lib=libraries[j]
           var idx=lib.lib_index  
           var prefix=lib_prefix[idx]
           if(lib.file_type!=null){
              if ( lib.file_type == "separate"){
                opt+=" --"+prefix+idx+"-1 "+"fastq:"+lib.fwd_reads.path+" "
                opt+=" --"+prefix+idx+"-2 "+"fastq:"+lib.rev_reads.path+" "
              }else{
                var suffix
                if ( lib.file_type == "interleaved"){
                  suffix="12"
                }
                if ( lib.file_type == "merged"){
                  suffix="m"
                }
                if ( lib.file_type == "unpaired"){
                  suffix="s"
                }
                opt+=" --"+prefix+idx+"-"+suffix+" "+"fastq:"+lib.reads.path+" "
              }
            }
          }  
           return opt  
         }
         EOF
         ##########################################


         #########################<DEBUG










         read -d '' CMD_READ2 << EOF
         ${
           var opt=""
           if (inputs.pacbio_reads!=null){
             for(var i=0; i<inputs.pacbio_reads.length;i++){
                var read=inputs.pacbio_reads[i]
                opt+=" --pacbio fastq:"+read.path+" "
             }
            }
           if (inputs.nanopore_reads!=null){
             for(var i=0; i<inputs.nanopore_reads.length;i++){
                var read=inputs.nanopore_reads[i]
                opt+=" --nanopore fastq:"+read.path+" "
             }
            }
           if (inputs.sanger_reads!=null){
             for(var i=0; i<inputs.sanger_reads.length;i++){
                var read=inputs.sanger_reads[i]
                opt+=" --sanger fastq:"+read.path+" "
             }
            }
           if (inputs.trusted_contigs!=null){
             for(var i=0; i<inputs.trusted_contigs.length;i++){
                var read=inputs.trusted_contigs[i]
                opt+=" --trusted-contigs fastq:"+read.path+" "
             }
            }
           if (inputs.untrusted_contigs!=null){
             for(var i=0; i<inputs.untrusted_contigs.length;i++){
                var read=inputs.untrusted_contigs[i]
                opt+=" --untrusted-contigs fastq:"+read.path+" "
             }
            }
           return opt  
         }
         EOF
         ##########################################
         read -d '' CMD_POST << EOF
           && python write_tsv.py < contigs.fasta > out_contig_stats.tab
           && python write_tsv.py < scaffolds.fasta > out_scaffold_stats.tab
         EOF
         ##########################################   
         # echo "CMD_BASE : \$CMD_BASE"  > zz.txt   \\
         #        && echo "CMD_READ1 : \$CMD_READ1"  >> zz.txt   \\
         #        && echo "CMD_READ2 : \$CMD_READ2"  >> zz.txt   \\
         #        && echo "CMD_POST : \$CMD_POST"   >> zz.txt
         COMMAND="\$CMD_BASE \$CMD_READ1 \$CMD_READ2 \$CMD_POST"
         COMMAND=\$(echo $COMMAND|tr -d '\\n')
         echo "\$COMMAND"  > run_spades.sh
         bash  ./run_spades.sh

CWL SPAdes From line 185 of tool/spades.cwl

- entryname: unicycler_launch.sh
  entry: |
    #!/bin/bash
    ###########################
    #      unicycler launcher
    ###########################

    ##preparing input files
    #check permission / chmod  is issues
    ${
      var fl=""
      var lncmd=""
      var fq1=""
      var fq2=""
      var lr=""

    //###################paired case
          if (inputs.fastq_file_type =="paired"  ){
           if( inputs.fastq1_type=='fastqsanger' ){
               fq1 = "fq1.fastq"
           }
           else if( inputs.fastq1_type=='fastqsanger.gz' ){
                fq1 = "fq1.fastq.gz"
           }
           if( inputs.fastq2_type=='fastqsanger' ){
               fq2 = "fq2.fastq"
            }
            else if( inputs.fastq2_type=='fastqsanger.gz' ){
                fq2 = "fq2.fastq.gz"
             }
             lncmd+="fq1='"+fq1+"'"
             lncmd+=" && "
             lncmd+="fq2='"+fq2+"'"
             lncmd+=" && "
             lncmd+=" ln -s '"+inputs.fastq1.path+"' $fq1 "
             lncmd+=" && "
             lncmd+=" ln -s '"+inputs.fastq2.path+"' $fq2  "

          }
     //###################single case

     if (inputs.fastq_file_type =="single"  ){
       if( inputs.fastq1_type=='fastqsanger' ){
           fq1 = "fq1.fastq"
       }
       else if( inputs.fastq1_type=='fastqsanger.gz' ){
            fq1 = "fq1.fastq.gz"
       }
       lncmd+="fq1='"+fq1+"'"
       lncmd+=" && "
       lncmd+=" ln -s '"+inputs.fastq1.path+"' $fq1 "
      }
      //####### long reads
       if (  inputs.sequence_long !== null) {
           if (inputs.sequence_long_type=='fastqsanger'){
                    lr = "lr.fastq"
           }
           else if (inputs.sequence_long_type=='fastqsanger.gz') {
                    lr = "lr.fastq.gz"
           }
           else if (inputs.sequence_longg_type=='fasta') {
                    lr = "lr.fasta"
           }
           lncmd+="lr='"+lr+"'"
           lncmd+=" && "
           lncmd+= " ln -s '"+inputs.sequence_long.path+"' '$lr' "
       }
       return lncmd
    }

    ##general options

    read -d '' GENERALOPT << EOF
    ${
     var opt=""
     //## General Unicycler Options section
     opt+=" --mode "+inputs.mode+" "
     opt+=" --min_fasta_length "+inputs.min_fasta_length+" "
     opt+=" --linear_seqs "+inputs.linear_seqs+" "

     if (inputs.min_anchor_seg_len  != null ){opt+=" --min_anchor_seg_len "+inputs.min_anchor_seg_len+" "}

     //## Spades Options section
     if(inputs.spades_no_correct==true){opt+=" --no_correct "}
     opt+=" --min_kmer_frac "+inputs.spades_min_kmer_frac+" "
     opt+=" --max_kmer_frac "+inputs.spades_max_kmer_frac+" "
     if (inputs.spades_kmers   != null){opt+=" --kmers "+inputs.spades_kmers+" "}

     opt+=" --kmer_count "+inputs.spades_kmer_count+" "
     opt+=" --depth_filter "+inputs.spades_depth_filter+" "
     if (inputs.spades_largest_component){opt+=" --largest_component "}
     //## Rotation Options section
     if(inputs.rotation_no_rotate == true){ opt+=" --no_rotate "}
     if (inputs.rotation_start_genes!=null){opt+=" --start_genes "+ inputs.rotation_start_genes.path+ " "}
     opt+=" --start_gene_id "+inputs.rotation_start_gene_id+" "
     opt+=" --start_gene_cov "+inputs.rotation_start_gene_cov+" "
     return opt
     }
    EOF

    ##additionnal option

    read -d '' ADDOPT << EOF
    ${

     var opt=""

     if (inputs.pilon_no_pilon  == true){ opt+=" --no_pilon " }
     if (inputs.pilon_min_polish_size  != null){opt+=" --min_polish_size "+inputs.pilon_min_polish_size + " "}
     //## Long Read Alignment Options
     if ( inputs.lr_align_contamination!=null){opt+=" --contamination "+inputs.lr_align_contamination + " "}
     opt+=" --scores "+inputs.lr_align_scores+" "
     if (inputs.lr_align_low_score != null){opt+=" --low_score "+inputs.lr_align_low_score+" "}
      return ''+ opt + ''
    }
    EOF

    ## Get location for pilon jar file

    ${
      var cmd=""
      cmd+="PILONJAR=/usr/share/java/pilon.jar "
      return cmd
    }

    ## Build Unicycler command
    ${

      var cmd_base=""
      var opt=""

      cmd_base+=" unicycler -t "+inputs.compute_slots+"  "
      cmd_base+=" -o ./  "
      cmd_base+=" --verbosity 3  "
      cmd_base+=" --pilon_path \$PILONJAR  "

     if ( inputs.fastq_file_type == "paired"){
            opt+=" -1 $fq1 -2 $fq2  "
     }
     else if ( inputs.fastq_file_type == "paired_collection"){
            opt+=" -1 $fq1 -2 $fq2  "
     }
     else if ( inputs.fastq_file_type == "single"){
        opt+=" -s $fq1 "
     }
     if (  inputs.sequence_long !== null) {
       opt+=" -l $lr "
     }

     //##  Unicycler command
     var cmdl=cmd_base+" "+opt+" \$GENERALOPT \$ADDOPT "

     return cmdl

     }

CWL oschmod Unicycler pilon From line 17 of tool/unicycler.cwl

baseCommand: bash

arguments:
- unicycler_launch.sh

hints:
  DockerRequirement:
    dockerPull: biocontainers/unicycler:v0.4.7dfsg-2-deb_cv1

CWL From line 362 of tool/unicycler.cwl

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Created: 1yr ago

Updated: 1yr ago

Maitainers: public

URL: https://github.com/fjrmoreews/cwl-workflow-SARS-CoV-2/blob/master/Assembly/workflow/assembly-wf-virus.cwl

Name: cwl-workflow-sars-cov-2

Version: Version 1

Badge:

Insert copied code into your website to add a link to this workflow.

License: MIT License

Keywords:

CWL Bandage pilon SPAdes Unicycler oschmod Genomics

Refs:

https://workflowhub.eu/workflows/3

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