Nextflow Modules
Showing module(s) with keyword "hmmer"
| Module | Kind | Keywords | Description |
|---|---|---|---|
| nf-core/fasta_hmmsearch_rank_fastas | Workflow | hmmer search rank fasta | Run hmmsearch and output separate fasta files for top scoring hits to each profile |
| nf-core/hmmer/eslalimask | Process | hmmer alignment mask | Mask multiple sequence alignments |
| nf-core/hmmer/eslalipid | Process | alignment msa pairwise identity sequence comparison hmmer easel | Calculate pairwise percent identity for all sequence pairs in a multiple sequence alignment |
| nf-core/hmmer/eslreformat | Process | sort hmmer reformat | reformats sequence files, see HMMER documentation for details. The module requires that the format is specified in ext.args in a config file, and that this comes last. See the tools help for possible values. |
| nf-core/hmmer/eslsfetch | Process | hmmer easel sequence retrieval subsequence extraction fasta | Retrieves one or more complete sequences or subsequences from a sequence file using its pre-built SSI index. The esl-sfetch utility is an Easel miniapp bundled with the HMMER package. This module only fetches: the SSI index must be produced beforehand by the sibling module `hmmer/eslsfetchindex`. The keyfile is used to fetch the named sequences (-f), or, with ext.args = '-C', parsed as a subsequence coordinate file (-Cf) to extract and rename subsequences. |
| nf-core/hmmer/eslsfetchindex | Process | hmmer easel indexing sequence retrieval ssi index fasta | Builds an SSI (sequence/subsequence index) file for a sequence file, using the esl-sfetch utility, an Easel miniapp bundled with the HMMER package (esl-sfetch --index). The resulting index lets esl-sfetch retrieve sequences from the file in constant time. This module is the indexing half of a pair: hmmer/eslsfetchindex builds the SSI index, hmmer/eslsfetch consumes it (or an equivalent one) to fetch sequences or subsequences. |
| 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/hmmemit | Process | hidden markov model HMM hmmer sequence emission simulation profile | emit sequences from a profile HMM |
| nf-core/hmmer/hmmfetch | Process | hidden Markov model HMM hmmer hmmfetch | extract hmm from hmm database file or create index for hmm database |
| nf-core/hmmer/hmmlogo | Process | hidden markov model HMM hmmer logo profile sequence logo | extract logo data from a profile HMM file to produce an HMM logo |
| nf-core/hmmer/hmmpress | Process | hidden Markov model HMM hmmer hmmpress hmmscan | compress and index profile database for hmmscan |
| 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 |
| nf-core/hmmer/hmmstat | Process | hidden markov model HMM hmmer statistics profile summary | display summary statistics for each profile HMM in an HMM database file |
| nf-core/macsyfinder/search | Process | genomics protein macromolecular systems hmmer search | Search for macromolecular systems in protein datasets using MacSyFinder |
| nf-core/mgnifam/generatefamilies | Process |