convert and then index CRAM -> BAM or BAM -> CRAM file
meta
Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
input
BAM/CRAM file
*.{bam,cram}
index
BAM/CRAM index file
*.{bai,crai}
fasta
Reference file to create the CRAM file
*.{fasta,fa}
alignment_index
filtered/converted BAM/CRAM file + index
*{.bam/cram,.bai/crai}
version
File containing software version
*.{version.txt}
SAMtools is a set of utilities for interacting with and post-processing short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li. These files are generated as output by short read aligners like BWA.
