See https://github.com/PacificBiosciences/pbmm2 for details. PacBio's wrapper for minimap2 can do bam input/output (so no converting to fastq), and also sort the output bam file on the fly, saving IO and run time.
Checklist
[x] Pull request details were added to CHANGELOG.md
See https://github.com/PacificBiosciences/pbmm2 for details. PacBio's wrapper for minimap2 can do bam input/output (so no converting to fastq), and also sort the output bam file on the fly, saving IO and run time.
Checklist
parameter_metafor each task is up to date.