mark duplicate alignments in a coordinate sorted file
meta:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end
input:file
BAM/CRAM/SAM file
*.{bam,cram,sam}
meta2:map
fasta:file
A reference genome in FASTA format
*.fasta
bam
*.bam:file
BAM file
*{.bam}
cram
*.cram:file
CRAM file
*{.cram}
sam
*.sam:file
SAM file
*{.sam}
versions
versions.yml:file
File containing software versions
versions.yml
Tools for dealing with SAM, BAM and CRAM files
