Fix for the crash of flye_medaka_workflow when running the POLISH workflow #1
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In its current state, the workflow crashes when going through POLISH. Medaka tries to call python, which expects to be in the
bin/
directory of the conda environment. But there is nopython
binary or link inbin/
. Addingpython
toenvironment.yml
fixes this problem.Medaka also needs the python module
ont_fast5_api
, which is not currently listed as a dependency. Soenvs\medaka.yml
now includesont-fast5-api
. Note that ifpython
is added toenvs\medaka.yml
, medaka is still unable to findont_fast_api
somehow. Ifpython
is added toenvironment.yml
, the module loads.With these two changes, the nextflow command listed in the onboarding tutorial works just fine.