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pontussk / PMDtools

Compute postmortem damage patterns and decontaminate ancient genomes
GNU General Public License v3.0
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`--first` parameter throws error in tagged release but not master branch #8

Open TCLamnidis opened 3 years ago

TCLamnidis commented 3 years ago

I am trying to add the possibility of using the --first option of pmdtools within nf-core/eager.

When using the tagged release of pmdtools (installed via conda) with the --first option I get the following error:

  Traceback (most recent call last):
    File "/opt/conda/envs/nf-core-eager-2.2.2dev/bin/pmdtools", line 1074, in <module>
      if n>0:
  NameError: name 'n' is not defined

In the release the code block that throws this error is: https://github.com/pontussk/PMDtools/blob/0.60/pmdtools.0.60.py#L1074-L1082

Changes to the code since the published release seem to fix this error, and testing of the pipeline with the master version (cc91fb8) indeed works as intended: https://github.com/pontussk/PMDtools/blob/master/pmdtools.0.60.py#L1075-L1081

Could you make a tagged release of the latest version of pmdtools which includes these changes?