Assemblosis: CWL based workflow to assemble haploid/diploid eukaryote genomes of non-model organisms

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CWL based workflow to assemble haploid/diploid eukaryote genomes of non-model organisms

The workflow is designed to use both PacBio long-reads and Illumina short-reads. The workflow first extracts, corrects, trims and decontaminates the long reads. Decontaminated trimmed reads are then used to assemble the genome and raw reads are used to polish it. Next, Illumina reads are cleaned and used to further polish the resultant assembly. Finally, the polished assembly is masked using inferred repeats and haplotypes are eliminated. The workflow uses BioConda and DockerHub to install required software and is therefore fully automated. In addition to final assembly, the workflow produces intermediate assemblies before and after polishing steps. The workflow follows the syntax for CWL v1.0.

Software tools used in this pipeline

Code Snippets

baseCommand: ["/home/smrtpipe.sh"]
arguments: []

CWL From line 43 of Run/arrow.cwl

baseCommand: [bowtie2]

CWL Bowtie 2 From line 70 of Run/bowtie2.cwl

baseCommand: ["canu", "-trim-assemble"]
arguments: []

CWL CANU From line 141 of Run/canuAssemble.cwl

baseCommand: ["canu", "-correct"]
arguments: []

CWL CANU From line 89 of Run/canuCorrect.cwl

baseCommand: ["centrifuge","-f"]
arguments:
- valueFrom: $(inputs.database.path)/nt
  prefix: -x
  position: 1
hints:
  - class: DockerRequirement
    dockerPull: quay.io/biocontainers/centrifuge:1.0.3--py27pl5.22.0_3

CWL Centrifuge From line 50 of Run/centrifuge.cwl

baseCommand: ["/home/haploMerger.sh"]
arguments: []

CWL From line 40 of Run/haplomerger.cwl

baseCommand: ["python","/home/Assemblosis/Run/hdf5check/hdf5Check.py"]

CWL From line 37 of Run/hdf5check.cwl

baseCommand: ["BuildDatabase"]
arguments:
- -name
- valueFrom: $(inputs.scaffolds.basename)
hints:
  - class: DockerRequirement
    dockerPull: quay.io/biocontainers/repeatmodeler:1.0.11--pl526_1

CWL From line 61 of Run/indexassembly.cwl

arguments:
- valueFrom: ${var r = []; for (var i = 0; i < inputs.bamPe.length; i++) { r.push("--frags"); r.push(inputs.bamPe[i].path); } return r; }
  position: 2

CWL From line 50 of Run/pilon.cwl

baseCommand: ["RepeatMasker"]
arguments: ["-dir", $(runtime.outdir)]
hints:
  - class: DockerRequirement
    dockerPull: quay.io/biocontainers/repeatmasker:4.0.9_p2--pl526_2
    #dockerPull: quay.io/biocontainers/repeatmasker:4.0.7--pl526_13
    #dockerPull: quay.io/biocontainers/repeatmasker:4.0.6--pl5.22.0_10

CWL RepeatMasker From line 79 of Run/repeatmasker.cwl

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

CWL From line 16 of Run/samindex.cwl

arguments:
- valueFrom: pe1.$(inputs.reads1.nameroot).fastq.gz
  position: 5
- valueFrom: unpe1.$(inputs.reads1.nameroot).fastq.gz
  position: 6
- valueFrom: pe2.$(inputs.reads2.nameroot).fastq.gz
  position: 7
- valueFrom: unpe2.$(inputs.reads2.nameroot).fastq.gz
  position: 8
- valueFrom: trim.log
  prefix: -trimlog 
  position: 16