#!/usr/bin/env cwl-runner cwlVersion: v1.0 class: Workflow requirements: - class: MultipleInputFeatureRequirement - class: InlineJavascriptRequirement - class: ScatterFeatureRequirement inputs: PATH: string[] tree: string[] scientific_name: string[] genome_fasta_name: string[] protein_fasta_name: string[] transcript_fasta_name: string[] cds_fasta_name: string[] gff_name: string[] deepPATH_genomic_fasta: string[] deepPATH_analyses: string[] deepPATH_bigwig: string[] MAIN_PATH: string steps: #step1 setup folder setup_folder: run: flow_reorganize_symlinks/setup_folder.cwl in: MAIN_PATH: MAIN_PATH tree: tree scientific_name: scientific_name out: [out_dummy] #step2 gzip - scaffold file scaffold_gzip: run: flow_reorganize_symlinks/scaffold_gzip.cwl in: in_dummy: setup_folder/out_dummy PATH: PATH tree: tree genome_fasta_name: genome_fasta_name deepPATH_genomic_fasta: deepPATH_genomic_fasta out: [out_dummy] #step3 symlink - scaffold file scaffold_symlink: run: flow_reorganize_symlinks/scaffold_symlink.cwl in: in_dummy: scaffold_gzip/out_dummy PATH: PATH tree: tree scientific_name: scientific_name genome_fasta_name: genome_fasta_name deepPATH_genomic_fasta: deepPATH_genomic_fasta MAIN_PATH: MAIN_PATH out: [out_dummy] #step4 symlink - analyses_protein files analyses_symlink_protein: run: flow_reorganize_symlinks/analyses_symlink_protein.cwl scatter: protein_fasta_name in: in_dummy: scaffold_symlink/out_dummy PATH: PATH tree: tree scientific_name: scientific_name protein_fasta_name: protein_fasta_name deepPATH_genomic_fasta: deepPATH_genomic_fasta deepPATH_analyses: deepPATH_analyses MAIN_PATH: MAIN_PATH out: [out_dummy] #step5 symlink - analyses files analyses_symlink: run: flow_reorganize_symlinks/analyses_symlink.cwl in: in_dummy: analyses_symlink_protein/out_dummy PATH: PATH tree: tree scientific_name: scientific_name genome_fasta_name: genome_fasta_name transcript_fasta_name: transcript_fasta_name cds_fasta_name: cds_fasta_name gff_name: gff_name deepPATH_genomic_fasta: deepPATH_genomic_fasta deepPATH_analyses: deepPATH_analyses MAIN_PATH: MAIN_PATH out: [out_dummy] #step6 gzip - bigwig files bigwig_gzip: run: flow_reorganize_symlinks/bigwig_gzip.cwl in: in_dummy: analyses_symlink/out_dummy PATH: PATH tree: tree genome_fasta_name: genome_fasta_name deepPATH_bigwig: deepPATH_bigwig out: [out_dummy] #step7 symlink - bigwig files-gaps bigwig_symlink-gaps: run: flow_reorganize_symlinks/bigwig_symlink-gaps.cwl in: in_dummy: bigwig_gzip/out_dummy PATH: PATH tree: tree scientific_name: scientific_name genome_fasta_name: genome_fasta_name deepPATH_bigwig: deepPATH_bigwig MAIN_PATH: MAIN_PATH out: [out_dummy] #step8 symlink - bigwig files-gc bigwig_symlink-gc: run: flow_reorganize_symlinks/bigwig_symlink-gc.cwl in: in_dummy: bigwig_symlink-gaps/out_dummy PATH: PATH tree: tree scientific_name: scientific_name genome_fasta_name: genome_fasta_name deepPATH_bigwig: deepPATH_bigwig MAIN_PATH: MAIN_PATH out: [out_dummy] #step9 symlink - assembly folder assembly_symlink: run: flow_reorganize_symlinks/assembly_symlink.cwl in: in_dummy: bigwig_symlink-gc/out_dummy tree: tree scientific_name: scientific_name MAIN_PATH: MAIN_PATH out: [] outputs: []