modules/muscle5_super5

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.

alignmsamultiple sequence alignment

https://github.com/nf-core/modules/[...]/modules/nf-core/muscle5/super5

Description

Input

name:type

description

pattern

`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.

Output

name:type

description

pattern

`alignment`

`meta:map`

Groovy Map containing sample information e.g. [ id:'test', single_end:false ]

`*.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`

`versions.yml:file`

File containing software versions

versions.yml

Tools

muscle -super5
Public Domain

Muscle v5 is a major re-write of MUSCLE based on new algorithms.

drive5.com/muscle5 drive5.com/muscle5/manual 10.1101/2021.06.20.449169

pigz

Parallel implementation of the gzip algorithm.

zlib.net/pigz zlib.net/pigz/pigz.pdf

modules/muscle5_super5

Description

Input

meta:map

fasta:file

compress:boolean

Output

alignment

meta:map

*.aln{.gz,}:file

versions

versions.yml:file

Tools

muscle -super5 Public Domain

pigz

`meta:map`

`fasta:file`

`compress:boolean`

`alignment`

`meta:map`

`*.aln{.gz,}:file`

`versions`

`versions.yml:file`

muscle -super5
Public Domain