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nf-core / oncoanalyser

A comprehensive cancer DNA/RNA analysis and reporting pipeline
https://nf-co.re/oncoanalyser
MIT License
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Add support for custom targeted panel #66

Open bounlu opened 2 months ago

bounlu commented 2 months ago

Description of feature

Currently the pipeline only supports tso500 panel for the targeted analysis with the pre-computed reference files given in the panel_data.config. It would be nice to allow custom panels and documentation how to prepare the corresponding reference files:

driver_gene_panel
sage_actionable_panel
sage_coverage_panel
pon_artefacts
target_region_bed
target_region_normalisation
target_region_ratios
target_region_msi_indels
isofox_tpm_norm
isofox_gene_ids
isofox_counts
isofox_gc_ratios
scwatts commented 2 months ago

We are trialing custom panel support in the 0.5.0, and I've put together some general high-level documentation on customising resource files that translates to panel data as well here.

You can also find information on generating custom panel resource files over on the hmftools GH here.

Is there any further documentation you would suggest having in the oncoanalyser GH for this? Keen to improve the docs for this