nf-core/pgdb
The ProteoGenomics database generation workflow creates different protein databases for ProteoGenomics data analysis.
cosmicgnomadprotein-databasesproteogenomicsproteomicspypgatk
This pipeline uses DSL1. It will not work with Nextflow versions after
Launch version 1.0.0 https://github.com/nf-core/pgdb 22.10.6.
Learn more.
Version history
Initial release of nf-core/pgdb, created with the nf-core template.
Added
The initial version of the pipeline features the following steps:
- (optional) ENSEMBL Reference proteomes included in final proteome
- Convert a Variant genome database like COSMIC or CBioPortal to proteomes
- Convert provided VCF to proteome database
- (optional) Generate the decoy database and attach it to the final proteome
Known issues
If you experience nextflow running forever after a failed step, try setting errorStrategy = terminate. See the corresponding nextflow issue.
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last release
about 4 years ago
last update
about 4 years ago
