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