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jts / ncov-tools

Small collection of tools for performing quality control on coronavirus sequencing data and genomes
MIT License
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get_qc.py getting passed unrecognized argument --run_name #26

Closed DarianHole closed 4 years ago

DarianHole commented 4 years ago

Hi again,

I've encountered a new issue with running the all_qc_summary command. In this, the get_qc.py script is failing as it is being passed the run name as the argument --run name <name> when that is not an argument that it has available to it.

Error in rule make_sample_qc_summary:
    jobid: 9
    output: qc_analysis/RV3258-20.summary.qc.tsv
    shell:
        ...

usage: get_qc.py [-h] [-c CONSENSUS] [-v VARIANTS] [-e COVERAGE] [-i]
                 [-m META] [-a ALLELES] [-s SAMPLE] [-p PLATFORM]
get_qc.py: error: unrecognized arguments: --run_name darian
rdeborja commented 4 years ago

After activating the conda environment, what version do you get when you type pip show ncov_parser? The latest version is 0.5.1 which contains the latest changes. After downloading, I've had to re-install the parser package times twice for some odd reason.

DarianHole commented 4 years ago

Oh that is the issue, I completely forgot I had to do that again

Thanks