Converts a SAM/BAM/CRAM file to FASTQ
meta
Groovy Map containing sample information e.g. [ id:‘test’, single_end
input
BAM/CRAM/SAM file
*.{bam,cram,sam}
interleave
Set true for interleaved fastq file
versions
File containing software versions
versions.yml
fastq
Compressed FASTQ file(s) with reads with either the READ1 or READ2 flag set in separate files.
*_{1,2}.fastq.gz
interleaved
Compressed FASTQ file with reads with either the READ1 or READ2 flag set in a combined file. Needs collated input file.
*_interleaved.fastq.gz
singleton
Compressed FASTQ file with singleton reads
*_singleton.fastq.gz
other
Compressed FASTQ file with reads with either both READ1 and READ2 flags set or unset
*_other.fastq.gz
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.
