Validate, filter, convert and perform various other operations on GFF files
meta{:bash}
:map
Groovy Map containing meta data e.g. [ id:‘test’ ]
gff{:bash}
:file
A reference file in either the GFF3, GFF2 or GTF format.
*.{gff, gtf}
fasta{:bash}
A multi-fasta file with the genomic sequences
*.{fasta,fa,faa,fas,fsa}
gtf{:bash}
*.gtf{:bash}
GTF file resulting from the conversion of the GFF input file if ‘-T’ argument is present
*.{gtf}
gffread_gff{:bash}
*.gff3{:bash}
GFF3 file resulting from the conversion of the GFF input file if ‘-T’ argument is absent
*.gff3
gffread_fasta{:bash}
*.fasta{:bash}
Fasta file produced when either of ‘-w’, ‘-x’, ‘-y’ parameters is present
*.fasta
versions_gffread{:bash}
${task.process}{:bash}
:string
The process the versions were collected from
gffread{:bash}
The tool name
gffread --version 2>&1{:bash}
:eval
The expression to obtain the version of the tool
versions{:bash}
GFF/GTF utility providing format conversions, region filtering, FASTA sequence extraction and more.
