/
heatmap-prepare.cwl
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heatmap-prepare.cwl
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cwlVersion: v1.0
class: Workflow
requirements:
- class: ScatterFeatureRequirement
- class: StepInputExpressionRequirement
- class: InlineJavascriptRequirement
inputs:
bam_file:
type: File[]
label: "BAM files"
doc: "Array of input BAM files"
fragment_size:
type: int[]
label: "Fragment sizes"
doc: "Array of fragment sizes"
total_reads:
type: int[]
label: "Total reads numbers"
doc: "Array of total reads number for downstream normalization"
outputs:
tag_folder:
type: Directory[]
label: "Tag directories"
doc: "Array of tag directories"
outputSource: make_tag_directory/output_tag_folder
steps:
make_tag_directory:
run: ../tools/homer-make-tag-directory.cwl
in:
bam_file: bam_file
fragment_size: fragment_size
total_reads: total_reads
scatter:
- bam_file
- fragment_size
- total_reads
scatterMethod: dotproduct
out: [output_tag_folder]
$namespaces:
s: http://schema.org/
$schemas:
- http://schema.org/docs/schema_org_rdfa.html
s:name: "heatmap-prepare"
s:downloadUrl: https://raw.githubusercontent.com/Barski-lab/workflows/master/workflows/heatmap-prepare.cwl
s:codeRepository: https://github.com/Barski-lab/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:misha.kotliar@gmail.com
s:sameAs:
- id: http://orcid.org/0000-0002-6486-3898
- class: s:Person
s:name: Andrey Kartashov
s:email: mailto:Andrey.Kartashov@cchmc.org
s:sameAs:
- id: http://orcid.org/0000-0001-9102-5681
doc: |
Workflow runs homer-make-tag-directory.cwl tool using scatter for the following inputs
- bam_file
- fragment_size
- total_reads
`dotproduct` is used as a `scatterMethod`, so one element will be taken from each array to construct each job:
1) bam_file[0] fragment_size[0] total_reads[0]
2) bam_file[1] fragment_size[1] total_reads[1]
...
N) bam_file[N] fragment_size[N] total_reads[N]
`bam_file`, `fragment_size` and `total_reads` arrays should have the identical order.
s:about: |
Runs homer-make-tag-directory.cwl with the scatter using dot product of the inputs bam_file, fragment_size and total_reads.