Nextflow Registry | nf-core/mafft/align@0.0.0-6c4ed3a

nf-core/mafft/align @ 0.0.0-6c4ed3a

Multiple sequence alignment using MAFFT

fasta msa multiple sequence alignment

Latest version: 0.0.0-6c4ed3a

Total downloads: 9

Source: nf-core/modules

Authors: @MillironX

Maintainers: @MillironX @Joon-Klaps

Multiple sequence alignment using MAFFT

Add the following snippet to your workflow script to include this module.

include { MAFFT_ALIGN } from 'nf-core/mafft/align'

MIT License

Process

`Name`	`MAFFT_ALIGN`

Input 7 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`fasta` file	FASTA file containing the sequences to align. May be gzipped or uncompressed. `*.{fa,fasta}{.gz,}`

#2 tuple

`meta2` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`add` file	FASTA file containing sequences to align to the sequences in `fasta` using `--add`. May be gzipped or uncompressed. `*.{fa,fasta}{.gz,}`

#3 tuple

`meta3` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`addfragments` file	FASTA file containing sequences to align to the sequences in `fasta` using `--addfragments`. May be gzipped or uncompressed. `*.{fa,fasta}{.gz,}`

#4 tuple

`meta4` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`addfull` file	FASTA file containing sequences to align to the sequences in `fasta` using `--addfull`. May be gzipped or uncompressed. `*.{fa,fasta}{.gz,}`

#5 tuple

`meta5` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`addprofile` file	FASTA file containing sequences to align to the sequences in `fasta` using `--addprofile`. May be gzipped or uncompressed. `*.{fa,fasta}{.gz,}`

#6 tuple

`meta6` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`addlong` file	FASTA file containing sequences to align to the sequences in `fasta` using `--addlong`. May be gzipped or uncompressed. `*.{fa,fasta}{.gz,}`

`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 3 channels

#1 fas tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.fas{.gz,}` file	Aligned sequences in FASTA format. May be gzipped or uncompressed. `*.fas{.gz,}`

#2 versions_pigz tuple

`${task.process}` string	The process name
`pigz` string	The tool name
`pigz --version 2>&1 \| sed 's/pigz //g'` eval	The expression to obtain the version of the tool

#3 versions_mafft tuple

Tool	Description	Homepage
mafft	Multiple alignment program for amino acid or nucleotide sequences based on fast Fourier transform	https://mafft.cbrc.jp/alignment/software/
pigz	Parallel implementation of the gzip algorithm.	https://zlib.net/pigz/