modules/
hmmer_hmmrank

Ranks hmmer/hmmsearch hits by score/e-value and, optionally, attaches per-hit domain coordinates -- reading the already-parsed, already-typed Parquet table(s) hmmer/formattsv

duckdb/table2parquet produce, rather than parsing raw hmmsearch tblout/domtblout text itself. The ranking and domain-coordinate merge run as DuckDB SQL (window functions, disk-spillable temp tables) instead of in-memory R/dplyr, so memory use no longer scales with the full width of every input row held at once.

hmmer hmmsearch rank duckdb

https://github.com/nf-core/modules/tree/master/modules/nf-core/hmmer/hmmrank

Description

Ranks hmmer/hmmsearch hits by score/e-value and, optionally, attaches per-hit domain coordinates -- reading the already-parsed, already-typed Parquet table(s) hmmer/formattsv

duckdb/table2parquet produce, rather than parsing raw hmmsearch tblout/domtblout text itself. The ranking and domain-coordinate merge run as DuckDB SQL (window functions, disk-spillable temp tables) instead of in-memory R/dplyr, so memory use no longer scales with the full width of every input row held at once.