created placeholder for the YAML+FASTA to TTL workflow

1 files changed, 31 insertions, 0 deletions

diff --git a/workflows/yamlfa2ttl/yamlfa2ttl.cwl b/workflows/yamlfa2ttl/yamlfa2ttl.cwl
new file mode 100644
index 0000000..2580794
--- /dev/null
+++ b/workflows/yamlfa2ttl/yamlfa2ttl.cwl
@@ -0,0 +1,31 @@
+#!/usr/bin/env cwl-runner
+
+cwlVersion: v1.1
+class: CommandLineTool
+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
+
+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
+    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
+