Update for HOPE processing #8
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jharenza
reviewed
Oct 21, 2024
naqvia
previously approved these changes
Oct 21, 2024
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This PR adds the HOPE cohort workflow and manifest files to
inputdirectory, and updates therun_fragpipe.shscript to take argument--cohortwith optionscptacandhope.See the wiki for instructions on how to mount either proteomics cavatica project: https://github.com/rokitalab/fragpipe/wiki/Mount-a-cavatica-project-on-EC2
Please run the following commands to ensure fragpipe is running as expected (making sure to mount appropriate cavatica project first):
bash run_fragpipe.sh --cohort cptac --run_subsetbash run_fragpipe.sh --cohort hope --run_subset