Merge branch 'bugfix/50-escape-workflow-parameters-for-bash' into 'development'

Resolve "Escape workflow parameters for bash"

Closes #50

See merge request !47

app/api/endpoints/workflow_version.py

@@ -289,7 +289,7 @@ async def download_workflow_documentation(
         if document is DocumentationEnum.PARAMETER_SCHEMA:
             path = workflow_mode.schema_path
 
-    return StreamingResponse(repo.download_file_stream(path, client))
+    return StreamingResponse(repo.download_file_stream(path, client), headers={"Cache-Control": "max-age=86400"})
 
 
 @router.post(

app/api/utils.py

 import json
 import re
+import shlex
 from io import BytesIO
 from tempfile import SpooledTemporaryFile
 from typing import TYPE_CHECKING, Any, BinaryIO, Dict, Optional, Sequence, Union
@@ -173,6 +174,10 @@ async def start_workflow_execution(
         f.write(json.dumps(parameters).encode("utf-8"))
         f.seek(0)
         s3.Bucket(name=settings.PARAMS_BUCKET).Object(key=params_file_name).upload_fileobj(f)
+    for key in parameters.keys():
+        if isinstance(parameters[key], str):
+            # Escape string parameters for bash shell
+            parameters[key] = shlex.quote(parameters[key]).replace("$", "\$")
 
     # Check if the there is an SCM file for the workflow
     scm_file_name = None

mako_templates/nextflow_command.template

@@ -18,5 +18,5 @@ ${nx_bin} run ${repo.repo_url} \
 % endif
 -revision ${repo.git_commit_hash} \
 % for param_name, param_value in parameters.items():
---${param_name} "${param_value}" \
+--${param_name} ${param_value} \
 % endfor