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YeoLab / merge_peaks

Pipeline for using IDR to produce a set of peaks given two replicate eCLIP peaks
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Error with cwltoil #9

Open Sanat-Mishra opened 3 years ago

Sanat-Mishra commented 3 years ago

I am getting the following error on running the yaml file with specfications:

RuntimeError: Please run with "toil-cwl-runner" instead of "cwltoil" (which has been removed)

However, in the main code on eCLIP_merge_peaks, I do not see toil-cwl-runner as an option, so I can't add it. Is this a version conflict?

byee4 commented 3 years ago

Hi,

We use TOIL 3.15.0a1 which is an older version that I've found to better support PBS/torque scheduling, but if your HPC uses SLURM or another scheduler, you might be able to get away with using a newer version and replacing cwltoil with cwl-toil-runner

Sanat-Mishra commented 3 years ago

Thanks for the reply. I'm guessing I'll have to replace cwltoil with with cwl-toil-runner at all places in the script?