On 8 Jun 2020, at 13:16, Keiran Raine <k...@sanger.ac.uk> wrote: > > Just a quick query. Where does samtools write the temporary files for the > collate step? Can I assume /tmp or the location defined by $TMPDIR?
At the moment if you want them to appear somewhere in particular other than /tmp (which is probably your smallest temp space!), you get to specify it each time using collate's optional <prefix> command line argument. See <https://github.com/samtools/samtools/issues/1172>. John _______________________________________________ Samtools-help mailing list Samtools-help@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/samtools-help
