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workflow.cwl
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workflow.cwl
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#!/usr/bin/env cwl-runner
cwlVersion: v1.0
class: Workflow
requirements:
- class: MultipleInputFeatureRequirement
- class: InlineJavascriptRequirement
inputs:
in_md5checksums: File
in_genomic_fasta: File
in_genomic_gff: File
in_protein_fasta: File[]
in_transcript_fasta: File
in_cds_fasta: File
steps:
extract_md5checksums:
run: extract_md5checksums.cwl
in:
in_txt: in_md5checksums
in_gz:
source: [in_genomic_fasta, in_genomic_gff, in_protein_fasta, in_transcript_fasta, in_cds_fasta]
linkMerge: merge_flattened
out:
[out_extract] #*.txt2 is the extracted version of md5checksums.txt
check_md5checksums:
run: check_md5checksums.cwl
in:
in_check: extract_md5checksums/out_extract
in_gz:
source: [in_genomic_fasta, in_genomic_gff, in_protein_fasta, in_transcript_fasta, in_cds_fasta]
linkMerge: merge_flattened
out:
[out_check]
gunzip_genomic_fasta:
run: gunzip_single.cwl
in:
in_dummy: check_md5checksums/out_check #dummy data to insure the order of execution
in_gz: in_genomic_fasta
out:
[out_gz]
gunzip_genomic_gff:
run: gunzip_single.cwl
in:
in_dummy: check_md5checksums/out_check #dummy data to insure the order of execution
in_gz: in_genomic_gff
out:
[out_gz]
gunzip_protein_fasta:
run: gunzip_multi.cwl
in:
in_dummy: check_md5checksums/out_check #dummy data to insure the order of execution
in_gz: in_protein_fasta
out:
[out_gz]
gunzip_transcript_fasta:
run: gunzip_single.cwl
in:
in_dummy: check_md5checksums/out_check #dummy data to insure the order of execution
in_gz: in_transcript_fasta
out:
[out_gz]
gunzip_cds_fasta:
run: gunzip_single.cwl
in:
in_dummy: check_md5checksums/out_check #dummy data to insure the order of execution
in_gz: in_cds_fasta
out:
[out_gz]
outputs:
OUT_extract:
type: File
outputSource: extract_md5checksums/out_extract
OUT_check:
type: File
outputSource: check_md5checksums/out_check
OUT_genomic_fasta:
type: File
outputSource: gunzip_genomic_fasta/out_gz
OUT_genomic_gff:
type: File
outputSource: gunzip_genomic_gff/out_gz
OUT_protein_fasta:
type: File[]
outputSource: gunzip_protein_fasta/out_gz
OUT_transcript_fasta:
type: File
outputSource: gunzip_transcript_fasta/out_gz
OUT_cds_fasta:
type: File
outputSource: gunzip_cds_fasta/out_gz