Parallel sorting and duplicate marking
meta:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]
bams:file
List containing 1 or more bam files
meta2:map
Groovy Map containing genome information e.g. [ id:‘genome’ ]
fasta:file
Reference genome in FASTA format (optional)
*.{fa,fasta,fna}
bam
*.bam:file
BAM file with duplicate reads marked/removed
*.bam
bam_index
*.bam.bai:file
BAM index file
*.bai
cram
*.cram:file
CRAM file with duplicate reads marked/removed
*.cram
metrics
*.metrics.txt:file
Duplicate metrics file generated by biobambam
*.{metrics.txt}
versions
versions.yml:file
File containing software versions
versions.yml
biobambam is a set of tools for early stage alignment file processing.
