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,}
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,}
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,}
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,}
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,}
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
name:type
description
pattern
fas
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,}
versions_mafft
${task.process}
:string
The process name
mafft
:string
The tool name
mafft --version 2>&1 | sed 's/ (.*) //g'
:eval
The tool version
versions_pigz
${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
Topics
name:type
description
pattern
versions
${task.process}
:string
The process name
mafft
:string
The tool name
mafft --version 2>&1 | sed 's/ (.*) //g'
:eval
The tool version
${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
Tools
mafft
BSD
Multiple alignment program for amino acid or nucleotide sequences based on fast Fourier transform
