/
workflow.cwl
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/
workflow.cwl
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#!/usr/bin/env cwl-runner
cwlVersion: v1.0
class: Workflow
requirements:
- class: SubworkflowFeatureRequirement
- class: MultipleInputFeatureRequirement
- class: InlineJavascriptRequirement
- class: ScatterFeatureRequirement
inputs:
in_dummy: File
PATH: string[]
tree: string[]
deepPATH_genomic_fasta: string[]
in_genomic_fasta: File
deepPATH_analyses: string[]
in_genomic_gff: File
in_protein_fasta: File[]
in_transcript_fasta: File
in_cds_fasta: File
in_assembly_readme: File
in_genePrediction_readme: File
#
deepPATH_apollo2_data: string[]
in_seq: Directory
in_tracks_conf: File
in_tracks: Directory
in_names: Directory
in_trackList_json: File
in_trackList_json_bak: File
#
deepPATH_bigwig: string[]
in_gaps_bigwig: File
in_gc_bigwig: File
steps:
cp_genomic_fasta:
run: cp_file.cwl
in:
PATH: PATH
tree: tree
deepPATH: deepPATH_genomic_fasta
in_data: in_genomic_fasta
out: []
cp_genomic_gff:
run: cp_file_4_annotation.cwl
in:
PATH: PATH
deepPATH_1: deepPATH_genomic_fasta
deepPATH_2: deepPATH_analyses
tree: tree
in_data: in_genomic_gff
out: []
cp_protein_fasta:
run: cp_file_4_annotation.cwl
scatter: in_data
in:
PATH: PATH
deepPATH_1: deepPATH_genomic_fasta
deepPATH_2: deepPATH_analyses
tree: tree
in_data: in_protein_fasta
out: []
cp_transcript_fasta:
run: cp_file_4_annotation.cwl
in:
PATH: PATH
deepPATH_1: deepPATH_genomic_fasta
deepPATH_2: deepPATH_analyses
tree: tree
in_data: in_transcript_fasta
out: []
cp_cds_fasta:
run: cp_file_4_annotation.cwl
in:
PATH: PATH
deepPATH_1: deepPATH_genomic_fasta
deepPATH_2: deepPATH_analyses
tree: tree
in_data: in_cds_fasta
out: []
cp_assembly_readme:
run: cp_file.cwl
in:
PATH: PATH
deepPATH: deepPATH_genomic_fasta
tree: tree
in_data: in_assembly_readme
out: []
cp_genePrediction_readme:
run: cp_file_4_annotation.cwl
in:
PATH: PATH
deepPATH_1: deepPATH_genomic_fasta
deepPATH_2: deepPATH_analyses
tree: tree
in_data: in_genePrediction_readme
out: []
#
cp_seq:
run: cp_dir.cwl
in:
PATH: PATH
tree: tree
deepPATH: deepPATH_apollo2_data
in_data: in_seq
out: []
cp_tracks_conf:
run: cp_file.cwl
in:
PATH: PATH
tree: tree
deepPATH: deepPATH_apollo2_data
in_data: in_tracks_conf
out: []
cp_tracks:
run: cp_dir.cwl
in:
PATH: PATH
tree: tree
deepPATH: deepPATH_apollo2_data
in_data: in_tracks
out: []
cp_names:
run: cp_dir.cwl
in:
PATH: PATH
tree: tree
deepPATH: deepPATH_apollo2_data
in_data: in_names
out: []
cp_trackList_json:
run: cp_file.cwl
in:
PATH: PATH
tree: tree
deepPATH: deepPATH_apollo2_data
in_data: in_trackList_json
out: []
cp_trackList_json_bak:
run: cp_file.cwl
in:
PATH: PATH
tree: tree
deepPATH: deepPATH_apollo2_data
in_data: in_trackList_json_bak
out: []
#
cp_gaps_bigwig:
run: cp_file.cwl
in:
PATH: PATH
tree: tree
deepPATH: deepPATH_bigwig
in_data: in_gaps_bigwig
out: []
cp_gc_bigwig:
run: cp_file.cwl
in:
PATH: PATH
tree: tree
deepPATH: deepPATH_bigwig
in_data: in_gc_bigwig
out: []
#
outputs: []