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PheLiM_workflow.cwl
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PheLiM_workflow.cwl
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cwlVersion: v1.0
class: Workflow
doc: |
Workflow to run PheLiM
## INPUTS
inputs:
off_target_predictions: File
huesken_table: File
siRNA_fasta: File
mRNA_fasta: File
phenotypes: File
output: string
HierClustering_executable: File
number_of_randomizations: int
number_of_cores: int
## OUTPUTS
outputs:
gene_contributions:
type: File
outputSource: PheLiM/output_contributions
## STEPS
steps:
Clustering_siRNA:
run: cluster/cluster.cwl
in:
siRNA_fasta: siRNA_fasta
HierClustering_executable: HierClustering_executable
out: [ output_clusters ]
Predict_OnTarget_Sites:
run: interactionmatrix/predictions/ontarget/get_BS_on_transcript.cwl
in:
mRNA_fasta:
siRNA_fasta:
out: [ output_sites ]
Calculate_OnTarget_Scores:
run: interactionmatrix/predictions/ontarget/
in:
huesken_table: husken_table
binding_sites: Predict_OnTarget_Sites/output_sites
out: [ output_ontarget_predictions ]
Predictions_to_Matrix:
run: interactionmatrix/prediction-to-matrix.cwl
in:
off_target_predictions: off_target_predictions
on_target_predictions: Calculate_OnTarget_Scores/output_on_target_predictions
out: [ output_matrix ]
PheLiM:
run: PheLiM.cwl
in:
siRNA_phenotype_associations: phenotypes
siRNA_clusters: Clustering_siRNA/output_clusters
interaction_matrix: Predictions_to_Matrix/output_matrix
output_file: output
ex_expressions_filter:
default:
number_of_cores:
default: 1
number_of_randomizations:
default: 30
out: [ output_contributions ]