Groovy Map containing sample information
e.g. [ id:‘test’]
fasta{:bash}
:file
Input sequences in FASTA format. May be gzipped or uncompressed.
*.{fa,fasta}{.gz,}
compress{:bash}
: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{:bash}
meta{:bash}
:map
Groovy Map containing sample information
e.g. [ id:'test']
*.aln{.gz,}{:bash}
:file
Alignment file. May be gzipped or uncompressed, depending on if compress is set to true or false.
*.{aln}{.gz,}
versions_kalign{:bash}
${task.process}{:bash}
:string
The name of the process
kalign{:bash}
:string
The name of the tool
kalign -v | sed "s/^.*kalign[[:space:]]*//"{:bash}
:eval
The expression to obtain the version of the tool
versions_pigz{:bash}
${task.process}{:bash}
:string
The name of the process
pigz{:bash}
:string
The name of the tool
pigz --version 2>&1 | sed "s/^.*pigz[[:space:]]*//"{:bash}
:eval
The expression to obtain the version of the tool
Topics
name:type
description
pattern
versions{:bash}
${task.process}{:bash}
:string
The name of the process
kalign{:bash}
:string
The name of the tool
kalign -v | sed "s/^.*kalign[[:space:]]*//"{:bash}
:eval
The expression to obtain the version of the tool
${task.process}{:bash}
:string
The name of the process
pigz{:bash}
:string
The name of the tool
pigz --version 2>&1 | sed "s/^.*pigz[[:space:]]*//"{:bash}
:eval
The expression to obtain the version of the tool
Tools
kalign
GPL v3
Kalign is a fast and accurate multiple sequence alignment algorithm.
