diff options
Diffstat (limited to 'workflows/yamlfa2ttl/yamlfa2ttl.cwl')
| -rw-r--r-- | workflows/yamlfa2ttl/yamlfa2ttl.cwl | 20 |
1 files changed, 7 insertions, 13 deletions
diff --git a/workflows/yamlfa2ttl/yamlfa2ttl.cwl b/workflows/yamlfa2ttl/yamlfa2ttl.cwl index 2913e99..563f00f 100644 --- a/workflows/yamlfa2ttl/yamlfa2ttl.cwl +++ b/workflows/yamlfa2ttl/yamlfa2ttl.cwl @@ -1,10 +1,3 @@ -~/.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 @@ -12,7 +5,7 @@ class: Workflow doc: "Workflow to go from YAML (metadata) + FASTA (sequence) to TTL (metadata)" inputs: - path_fasta: + path-fasta: type: string doc: input FASTA to validate @@ -20,14 +13,14 @@ inputs: type: string default: text/fasta - path_yaml: + path-yaml: type: string doc: input YAML to validate and convert in TTL steps: check_format: in: - path_fasta: path_fasta + path_fasta: path-fasta format_to_check: format_to_check doc: the input has to be a valid FASTA format file out: [] @@ -35,15 +28,16 @@ steps: check_sequence: in: - path_fasta: path_fasta + 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 + path_yaml: path-yaml + path_fasta: path-fasta + doc: check the input metadata information to put in the knowledge graph out: [] run: check_metadata.cwl |