From 2dbc025821bc5f686c423ff332a41e6cef892a77 Mon Sep 17 00:00:00 2001
From: samuelklee <samuelklee@users.noreply.github.com>
Date: Thu, 16 Mar 2023 11:56:31 -0400
Subject: [PATCH] Added documentation on OMP_NUM_THREADS and MKL_NUM_THREADS to
 GermlineCNVCaller and DetermineGermlineContigPloidy. (#8223)

---
 .../tools/copynumber/DetermineGermlineContigPloidy.java        | 3 +++
 .../hellbender/tools/copynumber/GermlineCNVCaller.java         | 3 +++
 2 files changed, 6 insertions(+)

diff --git a/src/main/java/org/broadinstitute/hellbender/tools/copynumber/DetermineGermlineContigPloidy.java b/src/main/java/org/broadinstitute/hellbender/tools/copynumber/DetermineGermlineContigPloidy.java
index f8f78c7e5d3..fcb93e202b9 100644
--- a/src/main/java/org/broadinstitute/hellbender/tools/copynumber/DetermineGermlineContigPloidy.java
+++ b/src/main/java/org/broadinstitute/hellbender/tools/copynumber/DetermineGermlineContigPloidy.java
@@ -64,6 +64,9 @@
  * the python environment is already set up. Otherwise, the environment must be created and activated as described in the
  * main GATK README.md file.</p>
  *
+ * <p>OpenMP and MKL parallelism can be controlled by setting the <code>OMP_NUM_THREADS</code> and <code>MKL_NUM_THREADS</code>
+ * environment variables, respectively.</p>
+ *
  * <p>Advanced users may wish to set the <code>THEANO_FLAGS</code> environment variable to override the GATK theano
  * configuration. For example, by running
  * <code>THEANO_FLAGS="base_compiledir=PATH/TO/BASE_COMPILEDIR" gatk DetermineGermlineContigPloidy ...</code>, users can specify
diff --git a/src/main/java/org/broadinstitute/hellbender/tools/copynumber/GermlineCNVCaller.java b/src/main/java/org/broadinstitute/hellbender/tools/copynumber/GermlineCNVCaller.java
index 301e2d7e275..83539dff444 100644
--- a/src/main/java/org/broadinstitute/hellbender/tools/copynumber/GermlineCNVCaller.java
+++ b/src/main/java/org/broadinstitute/hellbender/tools/copynumber/GermlineCNVCaller.java
@@ -89,6 +89,9 @@
  * the python environment is already set up. Otherwise, the environment must be created and activated as described in the
  * main GATK README.md file.</p>
  *
+ * <p>OpenMP and MKL parallelism can be controlled by setting the <code>OMP_NUM_THREADS</code> and <code>MKL_NUM_THREADS</code>
+ * environment variables, respectively.</p>
+ *
  * <p>Advanced users may wish to set the <code>THEANO_FLAGS</code> environment variable to override the GATK theano
  * configuration. For example, by running
  * <code>THEANO_FLAGS="base_compiledir=PATH/TO/BASE_COMPILEDIR" gatk GermlineCNVCaller ...</code>, users can specify