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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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Snakemake file #102

Open ksw9 opened 3 years ago

ksw9 commented 3 years ago

Hi, Thank you for a great tool that is so user friendly! I'm wondering where I can find a Snakefile or other information about sample processing. For example, I'm hoping to use the BAM files for other applications and it would be great to know the commands used to crate the BAM files (i.e. were duplicates removed, etc.). Thank you in advance!

dfornika commented 3 years ago

Hi @ksw9, this pipeline is implemented in Nextflow, a workflow management system similar to Snakemake. You can find the high-level workflow logic in the workflows directory, and specific commands in the modules directory.

This pipeline supports both Oxford Nanopore data and illumina data, but those data types follow different workflows.