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The framework is built to allow any number of pipelines. They are implemented using, and take a sample metadata file as input. Normally the pipelines are launched by the executor, upon detection up a new analysis.

Analysis types

In the standard offer, three types of analyses are offered: - basepipe: performs mapping, variant calling and QC - triopipe: performs join calling - annopipe: performs annotation and reporting

For a single sample, two analysis folders and metadata would have been created: one basepipe and one annopipe (which depends on the genepanel). For a trio, five analysis folders and metadata would have been created: three basepipe (one for each of the members), one triopipe (for joining them) and one annopipe.

Manual run

You can run a pipeline manually by running:

SETTINGS=/path/to/settings.json exe/pipeline/basepipe --analysis /path/to/my_analysis.analysis

How to create new pipeline

Since an analysis in the system consists of a single entry point (command), your pipeline must run the whole analysis from start to end in one step.

Under src/pipeline create: - a nextflow pipeline - mypipe-dependency: python script for checking dependencies - mypipe-post: python script for calling Quality Control and delivering files - a symlink lib to ../lib for utility classes Under exe/pipeline create an entry point script mypipe.

No modification of the executor is necessary.