meta map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
bams file	Input BAM file - must be coordinate sorted *.bam
bais file	BAM index file *.bai

meta2 map	Groovy Map containing reference information e.g. `[ id:'genome' ]`
fasta file	Reference genome FASTA file *.{fa,fasta,fna}

meta3 map	Groovy Map containing reference index information e.g. `[ id:'genome' ]`
fai file	Reference genome FASTA index file *.{fai}

meta4 map	Groovy Map containing target regions information e.g. `[ id:'targets' ]`
targets file	BED file containing target regions for realignment (optional) *.{bed}

meta5 map	Groovy Map containing GTF annotation information e.g. `[ id:'annotation' ]`
gtf file	GTF annotation file for RNA-seq data (optional) *.{gtf}

meta6 map	Groovy Map containing known indels information e.g. `[ id:'known_indels' ]`
known_indels file	VCF file containing known indels (optional) *.{vcf,vcf.gz}

meta map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
*.bam.bai file	BAM index file (optional) *.abra.bam.bai

meta map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
*.bam file	Realigned BAM file *.abra.bam

${task.process} string	The name of the process
abra2 string	The name of the tool
abra2 2>&1 | sed -n 's/.*Abra version: //p' eval	The expression to obtain the version of the tool