Nextflow Modules
Showing module(s) with keyword "hmmsearch"
| Module | Kind | Keywords | Description |
|---|---|---|---|
| nf-core/ampcombi | Process | antimicrobial peptides amps parsing reporting align macrel amplify hmmsearch neubi ampir DRAMP | A tool to parse and summarise results from antimicrobial peptides tools and present functional classification. |
| nf-core/ampcombi2/complete | Process | antimicrobial peptides amps parsing reporting align macrel amplify hmmsearch neubi ampir ampgram amptransformer DRAMP | A submodule that merges all output summary tables from ampcombi/parsetables in one summary file. |
| nf-core/ampcombi2/parsetables | Process | antimicrobial peptides amps parsing reporting align macrel amplify hmmsearch neubi ampir ampgram amptransformer DRAMP MMseqs2 InterProScan | A submodule that parses and standardizes the results from various antimicrobial peptide identification tools. |
| nf-core/bacphlip | Process | phage lifestyle temperate virulent bacphlip hmmsearch | A bacteriophage lifestyle prediction tool |
| nf-core/hmmer/formattsv | Process | hmmer hmmsearch tblout domtblout tsv | Convert HMMER's --tblout/--domtblout output to a clean, properly-delimited TSV |
| nf-core/hmmer/hmmbuild | Process | search hidden Markov model HMM hmmer hmmsearch | create an hmm profile from a multiple sequence alignment |
| nf-core/hmmer/hmmrank | Process | hmmer hmmsearch rank duckdb | 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. |
| nf-core/hmmer/hmmsearch | Process | Hidden Markov Model HMM hmmer hmmsearch | search profile(s) against a sequence database |