Docpatch

src/main/java/org/broadinstitute/hellbender/tools/genomicsdb/GenomicsDBImport.java

@@ -86,6 +86,7 @@
  *      -V data/gvcfs/father.g.vcf.gz \
  *      -V data/gvcfs/son.g.vcf.gz \
  *      --genomicsdb-workspace-path my_database \
+ *      --TMP-DIR=path/to/other/tmp \
  *      -L 20
  *  </pre>
  *
@@ -98,6 +99,7 @@
  *       --batch-size 50 \
  *       -L chr1:1000-10000 \
  *       --sample-name-map cohort.sample_map \
+ *       --TMP-DIR=path/to/other/tmp \
  *       --reader-threads 5
  *  </pre>
  *
@@ -117,6 +119,7 @@
  *     <li>At least one interval must be provided</li>
  *     <li>Input GVCFs cannot contain multiple entries for a single genomic position</li>
  *     <li>The --genomicsdb-workspace-path must point to a non-existent or empty directory.</li>
+ *     <li>GenomicsDBImport makes greedy use of /tmp by default, if your /tmp space is limited this will cause errors once /tmp has filled up. This happens quickly if the tool is running many intervals. It is therefore recommended to specify a different `--TMP-DIR`.</li>
  * </ul>
  *
  * <h3>Developer Note</h3>

src/main/java/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs.java

@@ -61,7 +61,8 @@
  * gatk --java-options "-Xmx4g" GenotypeGVCFs \
  *   -R Homo_sapiens_assembly38.fasta \
  *   -V gendb://my_database \
- *   -O output.vcf.gz
+ *   -O output.vcf.gz \
+ *   --TMP-DIR=path/to/other/tmp
  * </pre>
  *
  * <h3>Caveats</h3>
@@ -70,6 +71,7 @@
  * programs produce files that they call GVCFs but those lack some important information (accurate genotype likelihoods
  * for every position) that GenotypeGVCFs requires for its operation.</li>
  *   <li>Cannot take multiple GVCF files in one command.</li>
+ *   <li>Reading from a GenomicsDB workspace can fill up /tmp by default, causing confusing errors when scattering across many intervals. It is recommended to specify a `--TMP-DIR` if running this tool in combination with GenomicsDBImport.</li>
  * </ul>
  *
  * <h3>Special note on ploidy</h3>