nf-core/pgdb
The ProteoGenomics database generation workflow creates different protein databases for ProteoGenomics data analysis.
cosmicgnomadprotein-databasesproteogenomicsproteomicspypgatk
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
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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.