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add pipeline-name to looper arg group
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stolarczyk committed Jan 20, 2021
1 parent cde3791 commit 7257eca
Showing 1 changed file with 3 additions and 1 deletion.
4 changes: 3 additions & 1 deletion pypiper/utils.py
Original file line number Diff line number Diff line change
Expand Up @@ -813,7 +813,7 @@ def _determine_args(argument_groups, arguments, use_all_args=False):
"config": ["config"],
"checkpoint": ["stop-before", "stop-after"],
"resource": ["mem", "cores"],
"looper": ["config", "output-parent", "mem", "cores"],
"looper": ["config", "output-parent", "mem", "cores", "pipeline-name"],
"common": ["input", "sample-name"],
"ngs": ["sample-name", "input", "input2", "genome", "single-or-paired"],
"logmuse": LOGGING_CLI_OPTDATA.keys(),
Expand Down Expand Up @@ -914,6 +914,8 @@ def _add_args(parser, args, required):
"help": "Pipeline configuration file (YAML). "
"Relative paths are with respect to the "
"pipeline script."}),
"pipeline-name":
{"metavar": "PIPELINE_NAME", "help": "Name of the pipeline"},
"sample-name":
("-S", {"metavar": "SAMPLE_NAME",
"help": "Name for sample to run"}),
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