rrna_extraction
Description¶
Extraction of specific cmsearch-identified rRNA sequences from a fasta file using EASEL
Installation¶
ebi-metagenomics/rrna_extraction
nf-core modules -g https://www.github.com/ebi-metagenomics/nf-modules install rrna_extraction
Keywords: rRNA, fasta, easel, amplicon, cmsearch, covariance models
Components¶
This subworkflow uses the following components:
infernal/cmsearch(module)cmsearchtbloutdeoverlap(module)easel/eslsfetch(module)extractcoords(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 |
file | The input file containing Rfam database for use with cmsearch Structure: path(cm) | *.cm |
claninfo |
file | The input file containing the claninfo to use for cmsearchtbloutdeoverlap Structure: path(claninfo) | *.claninfo |
Output¶
| Name | Type | Description | Pattern |
|---|---|---|---|
cmsearch_deoverlap_out |
file | Channel containing cmsearchdeoverlap files Structure: [ val(meta), path(deoverlapped) ] | *.deoverlapped |
easel_out |
file | Channel containing extracted rRNA fasta files Structure: [ val(meta), path(fasta) ] | *.fasta |
ssu_fasta |
file | Fasta file containing the SSU sequences | *.fasta |
lsu_fasta |
file | Fasta file containing the LSU sequences | *.fasta |
concat_ssu_lsu_coords |
file | Space-separated concatenated file of coordinates of matches of both SSU and LSU | *.txt |
versions |
file | File containing software versions Structure: [ path(versions.yml) ] | versions.yml |