extractcoords
Description¶
Process output from easel-sfetch to extract SSU and LSU sequences
Pipelines¶
This module is used by the following pipelines:
Installation¶
ebi-metagenomics/extractcoords
nf-core modules -g https://www.github.com/ebi-metagenomics/nf-modules install extractcoords
Tools¶
extractcoords¶
Process output from easel-sfetch to extract SSU and LSU sequences, uses mgnify-pipelines-toolkit as conda environment
Input¶
| Name | Type | Description | Pattern |
|---|---|---|---|
meta |
map | Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ] |
- |
easel_coords_fasta |
file | Fasta file output from running esl-sfetch to extract sequences by name | *.fasta |
meta2 |
map | Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ] |
- |
matched_seqs_with_coords |
file | Space-separated cmsearchdeoverlap output formatted for use by esl-sfetch | *.txt |
separate_subunits |
boolean | Specify true to separate hits into the different RNA subunits | - |
Output¶
| Name | Type | Description | Pattern |
|---|---|---|---|
ssu_fasta |
file | - | |
lsu_fasta |
file | - | |
rrna_bacteria |
file | - | |
rrna_archaea |
file | - | |
eukarya |
file | - | |
fiveS_fasta |
file | - | |
five_eightS_fasta |
file | - | |
ncrna_fasta |
file | - | |
concat_ssu_lsu_coords |
file | - | |
versions |
file | - |
