diff options
Diffstat (limited to 'workflows/yamlfa2ttl/yamlfa2ttl.cwl')
| -rw-r--r-- | workflows/yamlfa2ttl/yamlfa2ttl.cwl | 20 |
1 files changed, 19 insertions, 1 deletions
diff --git a/workflows/yamlfa2ttl/yamlfa2ttl.cwl b/workflows/yamlfa2ttl/yamlfa2ttl.cwl index 143fc9d..2913e99 100644 --- a/workflows/yamlfa2ttl/yamlfa2ttl.cwl +++ b/workflows/yamlfa2ttl/yamlfa2ttl.cwl @@ -1,3 +1,10 @@ +~/.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 @@ -7,12 +14,16 @@ doc: "Workflow to go from YAML (metadata) + FASTA (sequence) to TTL (metadata)" inputs: path_fasta: type: string - doc: input fasta to validate + 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: @@ -29,4 +40,11 @@ steps: 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: [] |