rnaspades step dies with "AttributeError: module 'collections' has no attribute 'Hashable'" about transpi HOT 4 CLOSED

Hello @laninsky,

Could you pull again the repository. I see that your spades is v3.14.0. Currently, TransPi uses v3.15.3 where this issue is solved. See https://github.com/bioconda/bioconda-recipes/pull/31789/files

I did a test run and the pipeline is working fine with this version. Let me know how it goes.

Best,
Ramon

from transpi.

Thanks Ramon! I've pulled the new version and will let you know how it goes.

from transpi.

Hi Ramon - slightly different error is now stopping transpi (sorry - I know this is probably pretty trivial to edit the TransPi.nf file for, but I'm not fluent in either nextflow or python):

Error executing process > 'rna_spades_assembly (SRR6472974)'

Caused by:
  Failed to create Conda environment
  command: conda create --mkdir --yes --quiet --prefix /scale_wlg_nobackup/filesets/nobackup/uoo00105/transpi_conda/condaEnv/env-5ab1df8f4ffd36472969883031adc864 -c conda-forge bioconda::spades=3.15.3=h95f258a_1
  status : 1
  message:
    [Errno 2] No such file or directory: '/nesi/nobackup/uoo00105/alana.alexander/conda_pkgs/spades-3.15.3-h95f258a_1.tar.bz2'

from transpi.

Hi Ramon,

Just letting you know that the current test run I am doing with the repo pulled on Jan 18th seems to be working fine (the run is still in progress, but the rnaspades step has completed without an error), so going to go ahead and close this issue. Thanks for the help!

Alana

from transpi.