macs2 callpeak always writes to /tmp

[medmaca]

Currently no matter what you set $TMPDIR to the macs2 callpeak commands (MERGED_LIB_MACS2, MERGED_REP_MACS2) ignore this and write temporary files to /tmp. On some HPC this causes issues.

The modification of the two callpeak commands to include --tempdir allows the user to modify the temp directory, e.g.:

    macs2 callpeak \\
        -t ${bam[0]} \\
        $broad \\
        -f $format \\
        -g $params.macs_gsize \\
        -n $prefix \\
        $pileup \\
        --keep-dup all \\
        --tempdir $TMPDIR \\
        --nomodel

It would be good to allow users to pass such a path to the callpeak commands.