sample_id in the FASTA has to match the sample_id in the YAML yamlfa2ttl

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