Temp files not cleaned up?

[tseemann]

saffrontree -v -t 72 out1 *.gz

ls out1/
kmer_tree.newick 
 tmp4037372r  tmpafetgs9d  tmpeohwu5zr  tmpiktm7wbp  tmppa9dp89c  tmpt_y411ch  tmpyyyfzoaw
tmp02movqb_       tmp5oxycwr7  tmpag5o2eia  tmpfw22dg7c  tmpjzo7wosr  tmpptyagnj5  tmptcj9ezgv
tmp088xwgb3       tmp5quf9a99  tmpayt9w_t1  tmpgq4mqgol  tmpjzyyqup2  tmpqr8mgj48  tmptcjbxdw6
tmp0rtnxzvw       tmp6whv4zzf  tmpbxqrdi4x  tmpgt2dgdng  tmpk4fixrsj  tmpr6dt0s4r  tmpuddotnoe
tmp12rxjbjk       tmp8rq5trlz  tmpca6rh5yf  tmph1lvw4j5  tmpkgx_e7fv  tmprmvtd4af  tmpvflj5_qc
tmp14mwdjfs       tmp92g6__au  tmpccjyh3x3  tmphh7bwucq  tmpkwwksw2n  tmprtm8t0y5  tmpxuv7o3u3
tmp2viwsdve       tmp_jw5pw4h  tmpd8moshp7  tmphn_u97y8  tmpm27z1z7z  tmpslfuddqb  tmpy4qtrq01
tmp3pgnnosn       tmpa7u01vwt  tmpebdaapp6  tmphvdzidfa  tmpmphe0s6e  tmpsyhi1uqk  tmpyjxhs1ov

[andrewjpage]

If you use the verbose option (-v) all of the intermediate files are kept (documented in readme, but I'll make it clearer in the usage text of the script).

[tseemann]

Ok, I think you should have a -k --keep-files for that.

And could the folder names themselves be named meaningful?

[andrewjpage]

Added a separate option to keep the temp files with the directories more sensibly named.