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connor-lab / ncov2019-artic-nf

A Nextflow pipeline for running the ARTIC network's fieldbioinformatics tools (https://github.com/artic-network/fieldbioinformatics), with a focus on ncov2019
GNU Affero General Public License v3.0
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Adding mean coverage to qc.py #79

Open FredDodd6 opened 3 years ago

FredDodd6 commented 3 years ago

Adds mean coverage to qc.py. And an extra column in the csv for mean coverage.

m-bull commented 3 years ago

Thanks for the PR @FredDodd6.

Tests failed because csv produced by qc.py has to have "qc_pass: TRUE/FALSE" in the final column. The next stage of the nf process uses this column to send samples down different routes.

Should be a simple case of swapping these elements around in the dict.