This PR has some housekeeping prior to the 1.2.0 release. Changes:
Repo has been cleaned to remove an old fast5 which was lurking in the commit history and causing slow repo downloads. This improves the fix from https://github.com/artic-network/fieldbioinformatics/issues/38. It should be noted that anyone wanting to make a PR will need a fresh pull/fork of the repo from today.
Adds multiqc (artic fork) to the conda environment (via pip), which produces amplicon coverage plots and variant quality information. This closes https://github.com/artic-network/fieldbioinformatics/issues/51 as now amplicon coverage is computed from the align_trim report. Plots are now optionally produced by the user after the pipeline is run and can be collated across runs.
Deprecates plot_amplicon_depth script and removed associated dependencies. This has been a headache for pipeline users on HPC schedulers etc. Multiqc now replaces this functionality and the plotting is more accurate and optional.
Requires --medaka-model to be provided if --medaka is set.
This PR has some housekeeping prior to the 1.2.0 release. Changes:
Repo has been cleaned to remove an old fast5 which was lurking in the commit history and causing slow repo downloads. This improves the fix from https://github.com/artic-network/fieldbioinformatics/issues/38. It should be noted that anyone wanting to make a PR will need a fresh pull/fork of the repo from today.
Adds multiqc (artic fork) to the conda environment (via pip), which produces amplicon coverage plots and variant quality information. This closes https://github.com/artic-network/fieldbioinformatics/issues/51 as now amplicon coverage is computed from the align_trim report. Plots are now optionally produced by the user after the pipeline is run and can be collated across runs.
Deprecates plot_amplicon_depth script and removed associated dependencies. This has been a headache for pipeline users on HPC schedulers etc. Multiqc now replaces this functionality and the plotting is more accurate and optional.
Requires
--medaka-modelto be provided if--medakais set.Updated the docs.
Bumped the version to 1.2.0