easel_eslsfetch
Description¶
Extract fasta sequences by name from a cmsearchdeoverlap result
Pipelines¶
This module is used by the following pipelines:
Installation¶
ebi-metagenomics/easel/eslsfetch
nf-core modules -g https://www.github.com/ebi-metagenomics/nf-modules install easel/eslsfetch
Tools¶
easel¶
Easel is an ANSI C code library for computational analysis of biological sequences using probabilistic models.
Input¶
| Name | Type | Description | Pattern |
|---|---|---|---|
meta |
map | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
- |
fasta |
file | Fasta sequence file from amplicon sequencing | *.{fasta, fasta.gz, fa, fa.gz} |
cmsearch_deoverlap_out |
file | Tabular output from 'cmsearchtbloutdeoverlap' module | *.{tblout.deoverlap, tab, txt} |
Output¶
| Name | Type | Description | Pattern |
|---|---|---|---|
meta |
map | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
- |
easel_coords |
file | Fasta file output from running esl-sfetch to extract sequences by name | *.{fasta} |
matched_seqs_with_coords |
file | Space-separated cmsearchdeoverlap output formatted for use by esl-sfetch | *.txt |
versions |
file | File containing software versions | versions.yml |
