Groovy Map containing sample information
e.g. [ id:‘test’]
fasta
:file
Input sequences in FASTA format. 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
alignment
meta
:map
Groovy Map containing sample information
e.g. [ id:'test']
*.aln{.gz,}
:file
Alignment file. May be gzipped or uncompressed, depending on if compress is set to true or false.
*.{aln}{.gz,}
versions_kalign
${task.process}
:string
The name of the process
kalign
:string
The name of the tool
kalign -v | sed "s/^.*kalign[[:space:]]*//"
:eval
The expression to obtain the version of the tool
versions_pigz
${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
Topics
name:type
description
pattern
versions
${task.process}
:string
The name of the process
kalign
:string
The name of the tool
kalign -v | sed "s/^.*kalign[[:space:]]*//"
:eval
The expression to obtain the version of the tool
${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
Tools
kalign
GPL v3
Kalign is a fast and accurate multiple sequence alignment algorithm.
