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bismark-indices.cwl
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bismark-indices.cwl
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cwlVersion: v1.0
class: Workflow
inputs:
genome_label:
type: string?
label: "Genome label"
doc: "Genome label is used by web-ui to show label"
'sd:preview':
position: 1
genome_description:
type: string?
label: "Genome description"
doc: "Genome description is used by web-ui to show description"
'sd:preview':
position: 2
genome_details:
type: string?
label: "Genome details"
doc: "Genome details"
'sd:preview':
position: 3
genome_folder:
type: Directory
label: "Folder with the genome FASTA files"
doc: "Folder with the genome FASTA files (*.fa, *.fasta)"
outputs:
indices_folder:
type: Directory
label: "Bismark indices folder"
doc: "Bismark generated indices folder"
outputSource: prepare_indices/indices_folder
steps:
prepare_indices:
run: ../tools/bismark-prepare-genome.cwl
in:
genome_folder: genome_folder
out: [indices_folder]
$namespaces:
s: http://schema.org/
$schemas:
- http://schema.org/docs/schema_org_rdfa.html
s:name: "Generate genome indices for Bismark"
label: "Generate genome indices for Bismark"
s:alternateName: "Prepare indices for Bismark Methylation Pipeline. Bowtie2 aligner is used by default"
s:downloadUrl: https://raw.githubusercontent.com/datirium/workflows/master/workflows/bismark-indices.cwl
s:codeRepository: https://github.com/datirium/workflows
s:license: http://www.apache.org/licenses/LICENSE-2.0
s:isPartOf:
class: s:CreativeWork
s:name: Common Workflow Language
s:url: http://commonwl.org/
s:creator:
- class: s:Organization
s:legalName: "Cincinnati Children's Hospital Medical Center"
s:location:
- class: s:PostalAddress
s:addressCountry: "USA"
s:addressLocality: "Cincinnati"
s:addressRegion: "OH"
s:postalCode: "45229"
s:streetAddress: "3333 Burnet Ave"
s:telephone: "+1(513)636-4200"
s:logo: "https://www.cincinnatichildrens.org/-/media/cincinnati%20childrens/global%20shared/childrens-logo-new.png"
s:department:
- class: s:Organization
s:legalName: "Allergy and Immunology"
s:department:
- class: s:Organization
s:legalName: "Barski Research Lab"
s:member:
- class: s:Person
s:name: Michael Kotliar
s:email: mailto:michael.kotliar@cchmc.org
s:sameAs:
- id: http://orcid.org/0000-0002-6486-3898
doc: |
Run bismark_genome_preparation script to prepare indices for Bismark Methylation Analysis.
Bowtie2 aligner is used by default. The name of the output indices folder is equal to the genome folder name.