Auxiliary Toil features

Retrieving Intermediate files

Intermediate files are by default written to your TMP directory set by the TMP env variable. You should see many messages in the log say something like:

Redirecting logging to /juno/work/ci/nikhil/initial-setup/TMP/511cb20eb3df512ab906aea0f1bcc3f0/…

For the example above, the intermediate files will be located in this directory

/juno/work/ci/nikhil/initial-setup/TMP

If you do a tree of that directory, you can see that the intermediate files are inside.

.
├── ded20e739813590c861ec2e2bdf7373f
│   ├── 4db1
│   │   ├── 2192
│   │   │   ├── tmp4dl83x_w.tmp -> /juno/work/ci/nikhil/initial-setup/TMP/tmppbdggt72/files/no-job/file-968888cd7467497e9aef562d6644a485/GRCm38.fasta.bwt
│   │   │   ├── tmp53zlv1n9.tmp -> /juno/work/ci/nikhil/initial-setup/TMP/tmppbdggt72/files/no-job/file-24e17db5e6854c12803462af2dd9b434/GRCm38.fasta.pac
│   │   │   ├── tmp5cpn5a80.tmp -> /juno/work/ci/nikhil/initial-setup/TMP/tmppbdggt72/files/no-job/file-d14dcfb944d84c5d99e010124c8e014f/GRCm38.fasta.sa
│   │   │   ├── tmp5fhl9uj1.tmp -> /juno/work/ci/nikhil/initial-setup/TMP/tmppbdggt72/files/no-job/file-ac819ee927624171afd240354b1b7248/GRCm38.dict

You can get the intermediate files you need by running a find on the directory. For example, to get all the intermediate bams you can run:

find /juno/work/ci/nikhil/initial-setup/TMP -name "*.bam"