Groovy Map containing sample information
e.g. [ id:'test']
fasta{:bash}
:file
Input sequences in FASTA format
*.{fa,fasta,faa,fna}
meta2{:bash}
:map
Groovy Map containing tree information
e.g. [ id:'test_tree']
tree{:bash}
:file
Input guide tree in Newick format
*.{dnd}
hmm_in{:bash}
:file
HMM file for profile alignment
*.hmm
hmm_batch{:bash}
:file
specify HMMs for individual sequences
*.hmm
profile1{:bash}
:file
Pre-aligned multiple sequence file 1
*.{alnfaa,faa,fa,fasta}
profile2{:bash}
:file
Pre-aligned multiple sequence file 2
*.{alnfaa,faa,fa,fasta}
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, in gzipped fasta format
*.aln{.gz,}
versions_clustalo{:bash}
${task.process}{:bash}
:string
The name of the process
clustalo{:bash}
:string
The name of the tool
clustalo --version{: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
clustalo{:bash}
:string
The name of the tool
clustalo --version{: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
clustalo
GPL v2
Latest version of Clustal: a multiple sequence alignment program for DNA or proteins
