nf-core/viennarna/rnacofold @ 0.0.0-3fc6d40
Summary
calculate secondary structures of two RNAs with dimerization
Get started
Add the following snippet to your workflow script to include this module.
include { VIENNARNA_RNACOFOLD } from 'nf-core/viennarna/rnacofold'
License
MIT License
Process
Name
|
VIENNARNA_RNACOFOLD |
|---|
Input
1 channel
#1
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
rnacofold_fasta
file
|
A fasta file containing RNA or transcript sequences *.{fasta,fa}
|
Output
3 channels
#1
versions
versions.yml
file
|
File containing software versions versions.yml
|
|---|
#2
rnacofold_ps
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
*.ps
file
|
The text Output of RNAfold that contains the predicted secondary structure in postscript format *.{ps}
|
#3
rnacofold_csv
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
*.csv
file
|
The CSV Output of RNAcofold that has the predicted structure and energies *.{csv}
|
| Tool | Description | Homepage |
|---|---|---|
| viennarna | calculate secondary structures of two RNAs with dimerization The program works much like RNAfold, but allows one to specify two RNA sequences which are then allowed to form a dimer structure. RNA sequences are read from stdin in the usual format, i.e. each line of input corresponds to one sequence, except for lines starting with > which contain the name of the next sequence. To compute the hybrid structure of two molecules, the two sequences must be concatenated using the & character as separator. RNAcofold can compute minimum free energy (mfe) structures, as well as partition function (pf) and base pairing probability matrix (using the -p switch) Since dimer formation is concentration dependent, RNAcofold can be used to compute equilibrium concentrations for all five monomer and (homo/hetero)-dimer species, given input concentrations for the monomers. Output consists of the mfe structure in bracket notation as well as PostScript structure plots and “dot plot” files containing the pair probabilities, see the RNAfold man page for details. In the dot plots a cross marks the chain break between the two concatenated sequences. The program will continue to read new sequences until a line consisting of the single character @ or an end of file condition is encountered. | https://www.tbi.univie.ac.at/RNA/ |
| Version | 0.0.0-3fc6d40 |
|---|---|
| Commit ID | 6c4ed3a220310b905a1fc9d04f05be2e0837142b |
| Release Date | 22 Apr 2026 15:36:22 (UTC) |
| Download URL | https://registry.nextflow.io/api/v1/modules/nf-core%2Fviennarna%2Frnacofold/0.0.0-3fc6d40/download |
| OCI Store URL | https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/viennarna/rnacofold/blobs/sha256:c3605e6a50df9892ce53339549c8df3c719683d2f3f851441cf87bd51d3d3355 |
| Size | 2.9 KB |
| Checksum | sha256:c3605e6a50df9892ce53339549c8df3c719683d2f3f851441cf87bd51d3d3355 |
| Downloads | 3 |
| Version | Date | Status | Downloads | Size |
|---|---|---|---|---|
| 0.0.0-6c4ed3a | 23 Apr 2026 15:52:32 (UTC) | 3 | 2.9 KB | |
| 0.0.0-3fc6d40 | 22 Apr 2026 15:36:22 (UTC) | 3 | 2.9 KB | |
| 0.0.0-0c7146d | 08 Apr 2026 19:46:53 (UTC) | 3 | 2.9 KB |