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