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genomic-medicine-sweden / gms-artic

A nextflow pipeline with a GMS touch for running the ARTIC network's fieldbioinformatics tools (https://github.com/artic-network/fieldbioinformatics).
GNU Affero General Public License v3.0
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Updates and new additions #17

Closed JD2112 closed 3 years ago

JD2112 commented 3 years ago

The purpose of the code changes are as follows:

Standard test procedure

This version is a:

WHAT

  1. add freebayes to the pipeline for illumina analysis
  2. add a final report generated using for both Illumina and Nanopore analysis i. nextclade results ii. pangolin results
  3. pangolin updated to latest version (v3.1.4)
  4. separate pangolin container used for nanopore analysis
  5. add primer_scheme directory to the repo

WHY

  1. freebayes required for the analysis result
  2. final report will contains all analysis information for all analyzed, easy to view.
  3. needs update for pangolin
  4. havinf issues with pangolin (.RLock), resolve with separate container.
  5. primer_scheme directory needed for the primer trimming, particularly if different nanopore technologies used, artic/midnight/eden

HOW

  1. Freebayes - i. add freebayes with other requirements to the environment file [illumina] ii. add process to the /module/illumina.nf iii. add process to /workflows/illuminaNcov.nf iv. add process_gvcf.py /bin/process_gvcf.py

  2. for final report - i. add python script to /bin/ ii. add process to /modules/analysis.nf iii. add analysis to /workflows/*.nf

  3. environment file updated

  4. Singularity container for nanopore analysis and a separate pangolin container for nanopore analysis. i. changed the main.nf script for nanopolish

  5. need to add to the run script --scheme-directory primer_schemes/[artic/midnight/eden]/nCoV-2019/[Version number]/. details given in README.md

JD2112 commented 3 years ago

Looks good. Very nicely commented. A lot of files from primer-schemes, but that's just how it is sometimes 👍

thank you very much.