Hello all, About a year ago I stated wrapping the "samtools bam2fq" command from samtools v1.1 for use in Galaxy:
https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_bam2fq 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? https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/samtools Peter ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
