MarkDuplicates not respecting --TMP_DIR

[alexnater]

MarkDuplicates and probably other Picard tools don't seem to respect --TMP_DIR and keep writing a folder CSPI.tmpXXXX to /tmp. From the documentation I got the impression that setting --TMP_DIR /path/to/tmp is equivalent to setting --java-options "-Djava.io.tmpdir=/path/to/tmp". However, this is not the case and only in the latter case is the temporary directory respected.

[cmnbroad]

@alexnater This issue refers to a picard tool, but is in the GATK repository. Did you encounter this when launching MarkDuplicates via GATK, or via picard ? If via GATK, do you happen to know if this happens when using picard directly ? Also, please specify the version of (whichever one) you were using, since a similar issue was fixed a while back in picard.