converts FASTQ files to unmapped SAM/BAM/CRAM
meta
Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
[ id:'test', single_end:false ]
reads
fastq data to be converted to SAM/BAM/CRAM
*.{fastq,fq,fastq.gz,fq.gz}
versions
File containing software versions
versions.yml
sam
SAM file
*.sam
bam
Unaligned BAM file
*.bam
cram
Unaligned CRAM file
*.cram
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.
