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~/.config/guix/current/bin/guix environment -C guix --ad-hoc cwltool python python-biopython python-requests python-dateutil python-magic ruby
cwltool --preserve-environment PYTHONPATH yamlfa2ttl.cwl --path_fasta ~/bh20-seq-resource/example/sequence.fasta
cwltool --no-container --preserve-environment GUIX_ENVIRONMENT --preserve-environment PYTHONPATH yamlfa2ttl.cwl --path_fasta ~/bh20-seq-resource/example/sequence.fasta
#!/usr/bin/env cwl-runner
cwlVersion: v1.1
class: Workflow
doc: "Workflow to go from YAML (metadata) + FASTA (sequence) to TTL (metadata)"
inputs:
path_fasta:
type: string
doc: input FASTA to validate
format_to_check:
type: string
default: text/fasta
path_yaml:
type: string
doc: input YAML to validate and convert in TTL
steps:
check_format:
in:
path_fasta: path_fasta
format_to_check: format_to_check
doc: the input has to be a valid FASTA format file
out: []
run: check_format.cwl
check_sequence:
in:
path_fasta: path_fasta
doc: the input sequence has to be enough similar to the reference
out: []
run: check_sequence.cwl
check_metadata:
in:
path_yaml: path_yaml
doc: the input metadata information to put in the knowledge graph
out: []
run: check_metadata.cwl
outputs: []
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