genomic-medicine-sweden / gms-artic

A nextflow pipeline with a GMS touch for running the ARTIC network's fieldbioinformatics tools (https://github.com/artic-network/fieldbioinformatics).
GNU Affero General Public License v3.0
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Rich set to fixed version #73

Closed sofstam closed 1 year ago

sofstam commented 1 year ago

The purpose of the code changes are as follows:

*The production team in CG Stockholm got the following error during an analysis:

(cg_env) vincent.janvid@vincentjambp cg % docker run -it --entrypoint /bin/bash genomicmedicinesweden/gms-artic-nanopore:latest                                     
WARNING: The requested image's platform (linux/amd64) does not match the detected host platform (linux/arm64/v8) and no specific platform was requested
root@9a4104a14cf4:/# multiqc --version
Traceback (most recent call last):
  File "/opt/conda/envs/artic/bin/multiqc", line 6, in <module>
    from multiqc.__main__ import multiqc
  File "/opt/conda/envs/artic/lib/python3.6/site-packages/multiqc/__init__.py", line 16, in <module>
    from .multiqc import run
  File "/opt/conda/envs/artic/lib/python3.6/site-packages/multiqc/multiqc.py", line 29, in <module>
    from rich.syntax import Syntax
  File "/opt/conda/envs/artic/lib/python3.6/site-packages/rich/syntax.py", line 46, in <module>
    from .console import Console, ConsoleOptions, JustifyMethod, RenderResult
  File "/opt/conda/envs/artic/lib/python3.6/site-packages/rich/console.py", line 36, in <module>
    from rich._null_file import NULL_FILE
  File "/opt/conda/envs/artic/lib/python3.6/site-packages/rich/_null_file.py", line 69, in <module>
    NULL_FILE = NullFile()
  File "/opt/conda/envs/artic/lib/python3.6/typing.py", line 1231, in __new__
    return _generic_new(cls.__next_in_mro__, cls, *args, **kwds)
  File "/opt/conda/envs/artic/lib/python3.6/typing.py", line 1188, in _generic_new
    return base_cls.__new__(cls, *args, **kwds)
TypeError: Can't instantiate abstract class NullFile with abstract methods closed, mode, name

Standard test procedure

This version is a:

sofstam commented 1 year ago

Thanks for the review. Yes, one of the automatic tests is expected to fail, right @JD2112?

JD2112 commented 1 year ago

Yes, right. It's due to the Nextclade update. @sofstam Do you have any updates about the nextclade update integration?

sofstam commented 1 year ago

We are testing actually now :) @JD2112 I am merging this PR in the meanwhile.