Assembly Based ReAligner for next-generation sequencing data
meta
:map
Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]
[ id:'sample1', single_end:false ]
bams
:file
Input BAM file - must be coordinate sorted
*.bam
bais
BAM index file
*.bai
meta2
Groovy Map containing reference information e.g. [ id:'genome' ]
[ id:'genome' ]
fasta
Reference genome FASTA file
*.{fa,fasta,fna}
meta3
Groovy Map containing reference index information e.g. [ id:'genome' ]
fai
Reference genome FASTA index file
*.{fai}
meta4
Groovy Map containing target regions information e.g. [ id:'targets' ]
[ id:'targets' ]
targets
BED file containing target regions for realignment (optional)
*.{bed}
meta5
Groovy Map containing GTF annotation information e.g. [ id:'annotation' ]
[ id:'annotation' ]
gtf
GTF annotation file for RNA-seq data (optional)
*.{gtf}
meta6
Groovy Map containing known indels information e.g. [ id:'known_indels' ]
[ id:'known_indels' ]
known_indels
VCF file containing known indels (optional)
*.{vcf,vcf.gz}
bam
Realigned BAM file
*.abra.bam
bai
*.bam.bai
BAM index file (optional)
*.abra.bam.bai
versions
versions.yml
File containing software versions
