added check_metadata workflow and script

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: []