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-rw-r--r--workflows/yamlfa2ttl/yamlfa2ttl.cwl20
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: []