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