About a year ago I stated wrapping the "samtools bam2fq" command from samtools v1.1 for use in Galaxy:
That uncovered a number of bugs in "samtools bam2fq" which have resulted in two new commands "samtools fastq" and "samtools fasta" for converting a SAM/BAM/CRAM file into FASTQ or FASTA reads with the release of samtools 1.3.
When time permits, I had planned to update my wrapper to target samtools 1.3, probably as two separate tools which could potentially hook into the Galaxy datatype conversion framework?
Where would be the best place for them? Under tools-devteam?