detect_rna
Description¶
Extraction of specific cmsearch-identified RNA sequences from a fasta file using EASEL
Installation¶
nf-core modules -g https://www.github.com/ebi-metagenomics/nf-modules install detect_rna
Keywords: RNA, fasta, easel, cmsearch, cmscan, covariance models
Components¶
This subworkflow uses the following components:
infernal/cmsearch(module)infernal/cmscan(module)convertcmscantocmsearch(module)cmsearchtbloutdeoverlap(module)easel/eslsfetch(module)
Input¶
| Name | Type | Description | Pattern |
|---|---|---|---|
ch_fasta |
file | The input channel containing the fasta files Structure: [ val(meta), path(fasta) ] | *.{fasta, fasta.gz, fa, fa.gz} |
rfam |
directory | The folder containing Rfam database for use with cmsearch/cmscan Structure: path(cm) | - |
claninfo |
file | The input file containing the claninfo to use for cmsearchtbloutdeoverlap Structure: path(claninfo) | *.claninfo |
mode |
value | choose cmsearch or cmscan method to use | - |
Output¶
| Name | Type | Description | Pattern |
|---|---|---|---|
versions |
file | File containing software versions Structure: [ path(versions.yml) ] | versions.yml |
cmsearch_deoverlap_out |
- | ||
easel_out |
- |