nf-core/muscle5/super5 @ 0.0.0-6c4ed3a
Summary
Muscle is a program for creating multiple alignments of amino acid or nucleotide sequences. This particular module uses the super5 algorithm for very big alignments. It can permutate the guide tree according to a set of flags.
Get started
Add the following snippet to your workflow script to include this module.
include { MUSCLE5_SUPER5 } from 'nf-core/muscle5/super5'
License
MIT License
Name
|
MUSCLE5_SUPER5 |
|---|
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
fasta
file
|
Input sequences for alignment must be in FASTA format *.{fasta,fa,fna}
|
compress
boolean
|
Flag representing whether the output MSA should be compressed. Set to true to enable/false to disable compression. Compression is done using pigz, and is multithreaded. |
|---|
alignment
tuple
meta
map
|
Groovy Map containing sample information e.g. |
|---|---|
*.aln{.gz,}
file
|
Multiple sequence alignment produced in gzipped FASTA format. If '-perm all' is passed in ext.args, this will be multiple files per input! *.{aln.gz}
|
versions_pigz
tuple
${task.process}
string
|
The name of the process |
|---|---|
pigz
string
|
The name of the tool |
pigz --version 2>&1 | sed "s/^.*pigz[[:space:]]*//"
eval
|
The expression to obtain the version of the tool |
versions_muscle
tuple
${task.process}
string
|
The name of the process |
|---|---|
muscle
string
|
The name of the tool |
muscle -version | head -n 1 | cut -d " " -f 2 | sed "s/.linux64//"
eval
|
The expression to obtain the version of the tool |
| Tool | Description | Homepage |
|---|---|---|
| muscle -super5 | Muscle v5 is a major re-write of MUSCLE based on new algorithms. | https://drive5.com/muscle5/ |
| pigz | Parallel implementation of the gzip algorithm. | https://zlib.net/pigz/ |
| Version | 0.0.0-6c4ed3a |
|---|---|
| Commit ID | 6c4ed3a220310b905a1fc9d04f05be2e0837142b |
| Release Date | 23 Apr 2026 15:32:37 (UTC) |
| Download URL | https://registry.nextflow.io/api/v1/modules/nf-core%2Fmuscle5%2Fsuper5/0.0.0-6c4ed3a/download |
| OCI Store URL | https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/muscle5/super5/blobs/sha256:b3e206e633ea2f7a48ebc0119abe59734341c4d036e9dd8054a890cc432ecfce |
| Size | 3.2 KB |
| Checksum | sha256:b3e206e633ea2f7a48ebc0119abe59734341c4d036e9dd8054a890cc432ecfce |
| Downloads | 3 |
| Version | Date | Status | Downloads | Size |
|---|---|---|---|---|
| 0.0.0-6c4ed3a | 23 Apr 2026 15:32:37 (UTC) | 3 | 3.2 KB | |
| 0.0.0-3fc6d40 | 22 Apr 2026 15:23:15 (UTC) | 3 | 3.3 KB | |
| 0.0.0-0c7146d | 08 Apr 2026 19:20:32 (UTC) | 3 | 3.2 KB |