Evaluate alternatives for transforming bams to fastqs #121
Description
Description of feature
- https://scfbm.biomedcentral.com/articles/10.1186/1751-0473-9-13
- bedtools/bam2fastq
might be good replacements for samtools fastq.
Potential bug
samtools/collatefastq module might have the wrong logic for outputs for single-end data.