Workflow¶

Overview¶

TODO

A general overview of the workflow.

Tip

You can clik on the workflow nodes below to see the documentation for the relevant rules.

%%{init: { 'theme':'neutral' } }%% flowchart TB subgraph intake["Intake module"] sources[(fasta files)] sources --> combine end click sources,combine href "intake.html" combine --> alignment subgraph alignment["Alignment module"] MSA end click MSA href "alignment.html" alignment --> report MSA["multiple sequence alignment"] --> QC subgraph QC["Quality control module"] direction TB tree[maximum likelihood tree] --> phytest[Phytest checks] end click tree href "quality_control.html#tree" click phytest href "quality_control.html#phytest" QC --> Beast QC --> report subgraph Beast["Beast module"] direction TB XML["dynamic XML generation"] --> OnlineBEAST["add new sequences to previous run"] --> BEAST2 click XML href "beast.html#dynamicbeast" click OnlineBEAST href "beast.html#onlinebeast" click BEAST2 href "beast.html#beast" end Beast --> report{{Report generation}} click report href "report.html"

Modules & Rules¶

Modifying the workflow¶

When creating a McCoy project, you can optionally create a local copy of the Snakemake workflow and use this for your runs. This allows complete control over every rule and arbitrary modification of the pipeline:

mccoy create <project_name> \
    --reference <reference_fasta_file> \
    --template <beast2_template_file>
    --copy-workflow

The addition of the --copy-workflow flag will result in a new directory called workflow being placed in the project directory. This contains a complete copy of the Snakemake workflow that can be edited as needed. Any future use of the mccoy run command will automatically use this local copy.