nkrumm / nextflow-conifer-plots

Nextflow CoNIFER plots

A Nextflow pipeline for creating CoNIFER-adjusted CNV plots

Running locally

To run on a local NGS server: nextflow run main.nf -profile singularity --assay OPXv6 --input test_data/205R06_F01_OPXv6_NB0199.CNV_bins.txt

The above command will generate the CoNIFER-adjusted CNV plot CNV_plots/205R06_F01_OPXv6_NB0199.CNV.pdf

Currently supported assays:

• OPXv6

Porting to other environments

singularity.munge_v4.5 is a singularity build file for creating a container with all necessary dependencies.

Supply a --conifer_baselines_directory parameter pointed to a directory containing CoNIFER baseline files.