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Description
Hi, I just want to confirm that python 3.8 is needed for the latest pipeline but the yml file automatically installs python 3.7.8.
It is causing problems with the multiqc procedure. (seems like TypedDict needs python3.8 now?)
[ERROR ] multiqc : Oops! The 'interop' MultiQC module broke...
Please copy the following traceback and report it at https://github.com/ewels/MultiQC/issues
If possible, please include a log file that triggers the error - the last file found was:
None
Module interop raised an exception: Traceback (most recent call last):
File "/storage/group/dxl46/default/private/Shaoyi/QC/miniconda3/envs/corall/bin/multiqc", line 438, in multiqc
mod = config.avail_modules[this_module].load()
File "/storage/group/dxl46/default/private/Shaoyi/QC/miniconda3/envs/corall/lib/python3.7/site-packages/pkg_resources/init.py", line 2516, in load
return self.resolve()
File "/storage/group/dxl46/default/private/Shaoyi/QC/miniconda3/envs/corall/lib/python3.7/site-packages/pkg_resources/init.py", line 2522, in resolve
module = import(self.module_name, fromlist=['name'], level=0)
File "/storage/group/dxl46/default/private/Shaoyi/QC/miniconda3/envs/corall/lib/python3.7/site-packages/multiqc/modules/interop/init.py", line 2, in
from .interop import MultiqcModule
File "/storage/group/dxl46/default/private/Shaoyi/QC/miniconda3/envs/corall/lib/python3.7/site-packages/multiqc/modules/interop/interop.py", line 1, in
from multiqc.modules.base_module import BaseMultiqcModule
File "/storage/group/dxl46/default/private/Shaoyi/QC/miniconda3/envs/corall/lib/python3.7/site-packages/multiqc/modules/base_module.py", line 10, in
import markdown
File "/storage/group/dxl46/default/private/Shaoyi/QC/miniconda3/envs/corall/lib/python3.7/site-packages/markdown/init.py", line 42, in
from .core import Markdown, markdown, markdownFromFile
File "/storage/group/dxl46/default/private/Shaoyi/QC/miniconda3/envs/corall/lib/python3.7/site-packages/markdown/core.py", line 27, in
from . import util
File "/storage/group/dxl46/default/private/Shaoyi/QC/miniconda3/envs/corall/lib/python3.7/site-packages/markdown/util.py", line 32, in
from typing import TYPE_CHECKING, Generic, Iterator, NamedTuple, TypeVar, TypedDict, overload
ImportError: cannot import name 'TypedDict' from 'typing' (/storage/group/dxl46/default/private/Shaoyi/QC/miniconda3/envs/corall/lib/python3.7/typing.py)