From e9f73388c810c678a69ce23c925d7914ba99a251 Mon Sep 17 00:00:00 2001
From: AndreaGuarracino
Date: Tue, 5 Jan 2021 14:18:26 +0100
Subject: added check_format workflow and script

---
 workflows/yamlfa2ttl/yamlfa2ttl.cwl | 31 ++++++++++++-------------------
 1 file changed, 12 insertions(+), 19 deletions(-)

(limited to 'workflows/yamlfa2ttl/yamlfa2ttl.cwl')

diff --git a/workflows/yamlfa2ttl/yamlfa2ttl.cwl b/workflows/yamlfa2ttl/yamlfa2ttl.cwl
index 2580794..1dce9ca 100644
--- a/workflows/yamlfa2ttl/yamlfa2ttl.cwl
+++ b/workflows/yamlfa2ttl/yamlfa2ttl.cwl
@@ -1,31 +1,24 @@
 #!/usr/bin/env cwl-runner
 
 cwlVersion: v1.1
-class: CommandLineTool
+class: Workflow
 doc: "Workflow to go from YAML (metadata) + FASTA (sequence) to TTL (metadata)"
 
 inputs:
   path_fasta:
-    type: File
-    inputBinding:
-      position: 1
-  path_yaml:
-    type: File
-    inputBinding:
-      position: 2
+    type: string
+    doc: input fasta to validate
+
+  format_to_check:
+    type: string
+    default: text/fasta
 
 steps:
   check_format:
-    in: {path_fasta: path_fasta, path_valid_formats: '../../bh20sequploader/validation/formats', format_to_check: 'text/fasta'}
-    #out: true/false or nothing and it has to block the execution if the format is wrong
+    in:
+      path_fasta: path_fasta
+      format_to_check: format_to_check
+    out: []
     run: check_format.cwl
-  check_metadata:
-    # input and output
-    # run: check_metadata.cwl
-  check_header:
-    # id_fasta has to be equal to id_yaml
-    # run: check_header.cwl
-  check_sequence:
-    # The sequence has to be similar to the reference
-    # run: check_sequence.cwl
 
+outputs: []
-- 
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