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#!/usr/bin/env cwl-runner
cwlVersion: v1.1
class: CommandLineTool
doc: "Workflow to go from YAML (metadata) + FASTA (sequence) to TTL (metadata)"
inputs:
path_fasta:
type: File
inputBinding:
position: 1
path_yaml:
type: File
inputBinding:
position: 2
steps:
check_format:
in: {path_fasta: path_fasta, path_valid_formats: '../../bh20sequploader/validation/formats', format_to_check: 'text/fasta'}
#out: true/false or nothing and it has to block the execution if the format is wrong
run: check_format.cwl
check_metadata:
# input and output
# run: check_metadata.cwl
check_header:
# id_fasta has to be equal to id_yaml
# run: check_header.cwl
check_sequence:
# The sequence has to be similar to the reference
# run: check_sequence.cwl
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