Groovy Map containing sample information
e.g. [ id:'test']
fasta{:bash}
:file
Input sequences in FASTA format
*.{fa,fasta}
meta2{:bash}
:map
Groovy Map containing tree information
e.g. [ id:'test_tree']
tree{:bash}
:file
Input guide tree in Newick format
*.{dnd}
meta3{:bash}
:map
Groovy Map containing tree information
e.g. [ id:'test_infos']
template{:bash}
:file
T_coffee template file that maps sequences to the accessory information files to be used.
accessory_information{:bash}
:file
Accessory files to be used in the alignment. For example, it could be protein structures or secondary structures.
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 FASTA format. May be gzipped.
*.aln{.gz,}
lib{:bash}
meta{:bash}
:map
Groovy Map containing sample information
e.g. [ id:'test']
*.*lib{:bash}
:file
optional output, the library generated from the MSA file.
*.*lib
versions{:bash}
versions.yml{:bash}
:file
File containing software versions
versions.yml
Tools
tcoffee
GPL v3
A collection of tools for Computing, Evaluating and Manipulating Multiple Alignments of DNA, RNA, Protein Sequences and Structures.
