Tibanna helps you run your genomic pipelines on Amazon cloud (AWS). It is used by the 4DN DCIC (4D Nucleome Data Coordination and Integration Center) to process data. Tibanna supports CWL/WDL (w/ docker), Snakemake (w/ conda) and custom Docker/shell command.
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Add run_args to specify additional command line arguments #354
With this change, additional command line arguments can be specified in the tibanna job description that are passed to the cwltool, cromwell run, caper run commands.
This is necessary, e.g., for the ChipSeq pipeline that only runs using caper run ... --docker. In this case we can now specify "run_args": "--docker" in the job description.
With this change, additional command line arguments can be specified in the tibanna job description that are passed to the
cwltool,cromwell run,caper runcommands.This is necessary, e.g., for the ChipSeq pipeline that only runs using
caper run ... --docker. In this case we can now specify"run_args": "--docker"in the job description.