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-rw-r--r--workflows/yamlfa2ttl/yamlfa2ttl.cwl31
1 files changed, 31 insertions, 0 deletions
diff --git a/workflows/yamlfa2ttl/yamlfa2ttl.cwl b/workflows/yamlfa2ttl/yamlfa2ttl.cwl
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+++ b/workflows/yamlfa2ttl/yamlfa2ttl.cwl
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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
+