Groovy Map containing sample information
e.g. [ id:‘test’, single_end
]
fasta:file
FASTA file containing the sequences to align. May be gzipped or uncompressed.
*.{fa,fasta}{.gz,}
meta2:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end
]
add:file
FASTA file containing sequences to align to the sequences in fasta using --add. May be gzipped or uncompressed.
*.{fa,fasta}{.gz,}
meta3:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end
]
addfragments:file
FASTA file containing sequences to align to the sequences in fasta using --addfragments. May be gzipped or uncompressed.
*.{fa,fasta}{.gz,}
meta4:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end
]
addfull:file
FASTA file containing sequences to align to the sequences in fasta using --addfull. May be gzipped or uncompressed.
*.{fa,fasta}{.gz,}
meta5:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end
]
addprofile:file
FASTA file containing sequences to align to the sequences in fasta using --addprofile. May be gzipped or uncompressed.
*.{fa,fasta}{.gz,}
meta6:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end
]
addlong:file
FASTA file containing sequences to align to the sequences in fasta using --addlong. 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
fas
meta:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end
]
*.fas{.gz,}:file
Aligned sequences in FASTA format. May be gzipped or uncompressed.
*.fas{.gz,}
versions
versions.yml:file
File containing software versions
versions.yml
Tools
mafft
BSD
Multiple alignment program for amino acid or nucleotide sequences based on fast Fourier transform
