Indices builder from GBOL RDF (TTL)

public 1yr ago Version: Version 1 0 bookmarks

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indices-builder-from-gbol-rdf-ttl — View Workflow

Workflow to build different indices for different tools from a genome and transcriptome.

This workflow expects an (annotated) genome in GBOL ttl format.

Steps:

SAPP: rdf2gtf (genome fasta)
SAPP: rdf2fasta (transcripts fasta)
STAR index (Optional for Eukaryotic origin)
bowtie2 index
kallisto index

Code Snippets

baseCommand: [ fastqc ]

label: "FASTQC"
doc: |
    Performs quality control on FASTQ files

requirements:
 - class: InlineJavascriptRequirement
 - class: InitialWorkDirRequirement
   listing:
    - entry: "$({class: 'Directory', listing: []})"
      entryname: "FASTQC"
      writable: true

hints:
  SoftwareRequirement:
    packages:
      fastp :
        version: ["0.11.9"]
        specs: ["https://anaconda.org/bioconda/fastqc"]
  DockerRequirement:
    dockerPull: docker-registry.wur.nl/m-unlock/docker/fastqc:0.11.9

arguments: ["--outdir", "FASTQC"]

inputs:
  nanopore_reads: 
    type: File?
    doc: FastQ files list
    label: FASTQ files list
    inputBinding:
      position: 101
      prefix: --nano
  # nanopore_path: 
  #   type: string[]?
  #   doc: FastQ files list
  #   label: FASTQ files list
  #   inputBinding:
  #     position: 101
  #     prefix: --nano
  fastq:
    type: File[]?
    doc: FastQ file list
    label: FASTQ file list
    inputBinding:
      position: 100
  # fastq_path:
  #   # type: File[]?
  #   type: string[]?
  #   doc: FastQ file path list
  #   label: FastQ file paths
  #   inputBinding:
  #     position: 102
  threads:
    type: int?
    default: 1
    inputBinding:
      prefix: --threads

CWL FastQC fastp From line 6 of fastqc/fastqc.cwl

baseCommand: ["java", "-jar", "/NGTax-2.2.9.jar", "-ngtax", "-mapFile", "cwl_mapping_file.txt"]

arguments:
  - prefix: "-t"
    valueFrom: $(inputs.sample)_NG-Tax_$(inputs.for_read_len).ttl
  - prefix: "-b"
    valueFrom: $(inputs.sample)_NG-Tax_$(inputs.for_read_len).biom
  - prefix: "-mock3"
    valueFrom: $(inputs.mock3)
  - prefix: "-mock4"
    valueFrom: $(inputs.mock4)
  - prefix: "-fragment"
    valueFrom: $(inputs.fragment)

CWL From line 91 of ngtax/ngtax.cwl

baseCommand: ["python3", "/scripts/ngtax_to_tsv-fasta.py"]

arguments:
  - "-t"
  - $(inputs.input.path)
  - "-i"
  - $(inputs.identifier)
  - "-f"
  - $(inputs.fragment)  
  - "-m"
  - $(inputs.metadata)  