Compare, merge, annotate and estimate accuracy of generated gtf files
meta
:map
Groovy Map containing meta data e.g. [ id:‘test’, single_end:false ]
gtfs
:file
GTF/GFF files e.g. [ ‘file_1.gtf’, ‘file_2.gtf’ ]
*.{gtf,gff}
meta2
fasta
Genome reference fasta file (optional)
*.{fasta,fa}
fai
Index for fasta file
*.fai
meta3
reference_gtf
Reference annotation in gtf/gff format (optional)
annotated_gtf
*.annotated.gtf
Annotated gtf file when reference gtf is provided (optional)
combined_gtf
*.combined.gtf
Combined gtf file when multiple input files are provided (optional)
tmap
*.tmap
File listing the most closely matching reference transcript for each query transcript (optional)
refmap
*.refmap
File listing the reference transcripts with overlapping query transcripts (optional)
loci
*.loci
File with loci
stats
*.stats
File with stats for input transcripts as compared to reference alternatively stats for the combined gtf
tracking
*.tracking
This file matches transcripts up between samples
versions_gffcompare
${task.process}
:string
The name of the process
gffcompare
The name of the tool
gffcompare --version 2>&1 | sed "s/gffcompare v//"
:eval
The expression to obtain the version of the tool
versions
GffCompare by Geo Pertea
