From 347b8dce36832c6d3e379d81b3efefcbc88a3117 Mon Sep 17 00:00:00 2001
From: Peter Amstutz
Date: Thu, 30 Apr 2020 10:22:27 -0400
Subject: Wrap import script to run as a workflow

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
---
 scripts/import.cwl | 24 ++++++++++++++++++++++++
 1 file changed, 24 insertions(+)
 create mode 100644 scripts/import.cwl

(limited to 'scripts/import.cwl')

diff --git a/scripts/import.cwl b/scripts/import.cwl
new file mode 100644
index 0000000..81752c8
--- /dev/null
+++ b/scripts/import.cwl
@@ -0,0 +1,24 @@
+cwlVersion: v1.1
+class: CommandLineTool
+baseCommand: python3
+inputs:
+  scripts:
+    type: File
+    default:
+      class: File
+      location: import_to_arvados.py
+    inputBinding: {position: 1}
+  importScript:
+    type: File
+    default:
+      class: File
+      location: from_genbank_to_fasta_and_yaml.py
+    inputBinding: {position: 2}
+outputs: []
+requirements:
+  DockerRequirement:
+    dockerPull: bh20-seq-uploader/import
+  NetworkAccess:
+    networkAccess: true
+  WorkReuse:
+    workReuse: false
-- 
cgit v1.2.3


From 02ecf15cdc04270e06f2be7457bb1b284eeddc56 Mon Sep 17 00:00:00 2001
From: Peter Amstutz
Date: Thu, 30 Apr 2020 10:46:56 -0400
Subject: Import script fixes

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
---
 scripts/import.cwl           | 8 +++++++-
 scripts/import_to_arvados.py | 1 +
 2 files changed, 8 insertions(+), 1 deletion(-)

(limited to 'scripts/import.cwl')

diff --git a/scripts/import.cwl b/scripts/import.cwl
index 81752c8..d84516b 100644
--- a/scripts/import.cwl
+++ b/scripts/import.cwl
@@ -14,6 +14,12 @@ inputs:
       class: File
       location: from_genbank_to_fasta_and_yaml.py
     inputBinding: {position: 2}
+  dict:
+    type: Directory
+    default:
+      class: Directory
+      location: dict_ontology_standardization
+    inputBinding: {position: 3}
 outputs: []
 requirements:
   DockerRequirement:
@@ -21,4 +27,4 @@ requirements:
   NetworkAccess:
     networkAccess: true
   WorkReuse:
-    workReuse: false
+    enableReuse: false
diff --git a/scripts/import_to_arvados.py b/scripts/import_to_arvados.py
index 07b7d71..78cd13d 100644
--- a/scripts/import_to_arvados.py
+++ b/scripts/import_to_arvados.py
@@ -4,6 +4,7 @@ import glob
 import sys
 
 os.chdir(os.environ["TMPDIR"])
+os.symlink(sys.argv[2], "dict_ontology_standardization")
 subprocess.run(sys.argv[1])
 
 os.chdir("fasta_and_yaml")
-- 
cgit v1.2.3