Sort SAM/BAM/CRAM file
meta :map
Groovy Map containing sample information e.g. [ id:‘test’, single_end
bam :file
BAM/CRAM/SAM file
*.{bam,cram,sam}
fasta :file
Reference genome fasta file
*.{fasta,fa}
Sorted BAM/CRAM/SAM file
bai :file
BAM/CRAM/SAM index file
*.{bai,crai,sai}
crai :file
stats :file
File containing samtools stats output
*.{stats}
flagstat :file
File containing samtools flagstat output
*.{flagstat}
idxstats :file
File containing samtools idxstats output
*.{idxstats}
versions :file
File containing software versions
versions.yml
