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Resolve "Use parameter file for nextflow instead of CLI parameters"

8 files
+ 17
21
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import json
import shlex
import time
from asyncio import sleep as async_sleep
from enum import StrEnum, unique
@@ -138,10 +137,6 @@ async def start_workflow_execution(
handle=f,
s3=s3,
)
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
if scm_file_id is not None:
@@ -154,7 +149,6 @@ async def start_workflow_execution(
nextflow_script = ResourceScriptsTemplates.NEXTFLOW_COMMAND.render(
repo=git_repo,
parameters=parameters,
execution_id=execution.execution_id,
settings=settings,
scm_file_id=scm_file_id,
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