Nextflow Modules
Showing module(s) with keyword "sequence retrieval"
| Module | Keywords | Description |
|---|---|---|
| nf-core/hmmer/eslsfetch | 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 | 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. |