diff --git a/core/src/main/scala/org/bdgenomics/cannoli/BcftoolsNorm.scala b/core/src/main/scala/org/bdgenomics/cannoli/BcftoolsNorm.scala
index 29f6de3..b65b3de 100644
--- a/core/src/main/scala/org/bdgenomics/cannoli/BcftoolsNorm.scala
+++ b/core/src/main/scala/org/bdgenomics/cannoli/BcftoolsNorm.scala
@@ -40,8 +40,8 @@ class BcftoolsNormArgs extends Args4jBase {
   @Args4jOption(required = false, name = "-executable", usage = "Path to the BCFtools executable. Defaults to bcftools.")
   var executable: String = "bcftools"
 
-  @Args4jOption(required = false, name = "-image", usage = "Container image to use. Defaults to quay.io/biocontainers/bcftools:1.6--0.")
-  var image: String = "quay.io/biocontainers/bcftools:1.6--0"
+  @Args4jOption(required = false, name = "-image", usage = "Container image to use. Defaults to quay.io/biocontainers/bcftools:1.9--h4da6232_0.")
+  var image: String = "quay.io/biocontainers/bcftools:1.9--h4da6232_0"
 
   @Args4jOption(required = false, name = "-sudo", usage = "Run via sudo.")
   var sudo: Boolean = false
diff --git a/core/src/main/scala/org/bdgenomics/cannoli/BedtoolsIntersect.scala b/core/src/main/scala/org/bdgenomics/cannoli/BedtoolsIntersect.scala
index 02e3502..d239f8b 100644
--- a/core/src/main/scala/org/bdgenomics/cannoli/BedtoolsIntersect.scala
+++ b/core/src/main/scala/org/bdgenomics/cannoli/BedtoolsIntersect.scala
@@ -48,8 +48,8 @@ class BedtoolsIntersectArgs extends Args4jBase {
   @Args4jOption(required = false, name = "-executable", usage = "Path to the Bedtools executable. Defaults to bedtools.")
   var executable: String = "bedtools"
 
-  @Args4jOption(required = false, name = "-image", usage = "Container image to use. Defaults to quay.io/biocontainers/bedtools:2.27.1--0.")
-  var image: String = "quay.io/biocontainers/bedtools:2.27.1--0"
+  @Args4jOption(required = false, name = "-image", usage = "Container image to use. Defaults to quay.io/biocontainers/bedtools:2.27.1--he941832_2.")
+  var image: String = "quay.io/biocontainers/bedtools:2.27.1--he941832_2"
 
   @Args4jOption(required = false, name = "-sudo", usage = "Run via sudo.")
   var sudo: Boolean = false
diff --git a/core/src/main/scala/org/bdgenomics/cannoli/Bowtie.scala b/core/src/main/scala/org/bdgenomics/cannoli/Bowtie.scala
index 6444050..c92b46a 100644
--- a/core/src/main/scala/org/bdgenomics/cannoli/Bowtie.scala
+++ b/core/src/main/scala/org/bdgenomics/cannoli/Bowtie.scala
@@ -36,8 +36,8 @@ class BowtieArgs extends Args4jBase {
   @Args4jOption(required = false, name = "-executable", usage = "Path to the Bowtie executable. Defaults to bowtie.")
   var executable: String = "bowtie"
 
-  @Args4jOption(required = false, name = "-image", usage = "Container image to use. Defaults to quay.io/biocontainers/bowtie:1.2.1.1--py27pl5.22.0_0.")
-  var image: String = "quay.io/biocontainers/bowtie:1.2.1.1--py27pl5.22.0_0"
+  @Args4jOption(required = false, name = "-image", usage = "Container image to use. Defaults to quay.io/biocontainers/bowtie:1.2.2--py27h2d50403_1.")
+  var image: String = "quay.io/biocontainers/bowtie:1.2.2--py27h2d50403_1"
 
   @Args4jOption(required = false, name = "-sudo", usage = "Run via sudo.")
   var sudo: Boolean = false
diff --git a/core/src/main/scala/org/bdgenomics/cannoli/Bwa.scala b/core/src/main/scala/org/bdgenomics/cannoli/Bwa.scala
index e333cdd..0b1b993 100644
--- a/core/src/main/scala/org/bdgenomics/cannoli/Bwa.scala
+++ b/core/src/main/scala/org/bdgenomics/cannoli/Bwa.scala
@@ -43,8 +43,8 @@ class BwaArgs extends Args4jBase {
   @Args4jOption(required = false, name = "-executable", usage = "Path to the BWA executable. Defaults to bwa.")
   var executable: String = "bwa"
 
-  @Args4jOption(required = false, name = "-image", usage = "Container image to use. Defaults to quay.io/biocontainers/bwa:0.7.17--pl5.22.0_0.")
-  var image: String = "quay.io/biocontainers/bwa:0.7.17--pl5.22.0_0"
+  @Args4jOption(required = false, name = "-image", usage = "Container image to use. Defaults to quay.io/biocontainers/bwa:0.7.17--ha92aebf_3.")
+  var image: String = "quay.io/biocontainers/bwa:0.7.17--ha92aebf_3"
 
   @Args4jOption(required = false, name = "-sudo", usage = "Run via sudo.")
   var sudo: Boolean = false
diff --git a/core/src/main/scala/org/bdgenomics/cannoli/Freebayes.scala b/core/src/main/scala/org/bdgenomics/cannoli/Freebayes.scala
index e7132c7..dc4044e 100644
--- a/core/src/main/scala/org/bdgenomics/cannoli/Freebayes.scala
+++ b/core/src/main/scala/org/bdgenomics/cannoli/Freebayes.scala
@@ -39,8 +39,8 @@ class FreebayesArgs extends Args4jBase {
   @Args4jOption(required = false, name = "-executable", usage = "Path to the Freebayes executable. Defaults to freebayes.")
   var executable: String = "freebayes"
 
-  @Args4jOption(required = false, name = "-image", usage = "Container image to use. Defaults to quay.io/biocontainers/freebayes:1.1.0.46--htslib1.6_2.")
-  var image: String = "quay.io/biocontainers/freebayes:1.1.0.46--htslib1.6_2"
+  @Args4jOption(required = false, name = "-image", usage = "Container image to use. Defaults to quay.io/biocontainers/freebayes:1.2.0--py27h82df9c4_3.")
+  var image: String = "quay.io/biocontainers/freebayes:1.2.0--py27h82df9c4_3"
 
   @Args4jOption(required = false, name = "-sudo", usage = "Run via sudo.")
   var sudo: Boolean = false
diff --git a/core/src/main/scala/org/bdgenomics/cannoli/Minimap2.scala b/core/src/main/scala/org/bdgenomics/cannoli/Minimap2.scala
index 1129985..5d7263c 100644
--- a/core/src/main/scala/org/bdgenomics/cannoli/Minimap2.scala
+++ b/core/src/main/scala/org/bdgenomics/cannoli/Minimap2.scala
@@ -36,8 +36,8 @@ class Minimap2Args extends Args4jBase {
   @Args4jOption(required = false, name = "-executable", usage = "Path to the Minimap2 executable. Defaults to minimap2.")
   var executable: String = "minimap2"
 
-  @Args4jOption(required = false, name = "-image", usage = "Container image to use. Defaults to quay.io/biocontainers/minimap2:2.9--1.")
-  var image: String = "quay.io/biocontainers/minimap2:2.9--1"
+  @Args4jOption(required = false, name = "-image", usage = "Container image to use. Defaults to quay.io/biocontainers/minimap2:2.14--ha92aebf_0.")
+  var image: String = "quay.io/biocontainers/minimap2:2.14--ha92aebf_0"
 
   @Args4jOption(required = false, name = "-sudo", usage = "Run via sudo.")
   var sudo: Boolean = false
diff --git a/core/src/main/scala/org/bdgenomics/cannoli/SamtoolsMpileup.scala b/core/src/main/scala/org/bdgenomics/cannoli/SamtoolsMpileup.scala
index e62f2bb..516e759 100644
--- a/core/src/main/scala/org/bdgenomics/cannoli/SamtoolsMpileup.scala
+++ b/core/src/main/scala/org/bdgenomics/cannoli/SamtoolsMpileup.scala
@@ -37,8 +37,8 @@ class SamtoolsMpileupArgs extends Args4jBase {
   @Args4jOption(required = false, name = "-executable", usage = "Path to the samtools executable. Defaults to samtools.")
   var executable: String = "samtools"
 
-  @Args4jOption(required = false, name = "-docker_image", usage = "Container image to use. Defaults to quay.io/biocontainers/samtools:1.6--0.")
-  var image: String = "quay.io/biocontainers/samtools:1.6--0"
+  @Args4jOption(required = false, name = "-docker_image", usage = "Container image to use. Defaults to quay.io/biocontainers/samtools:1.9--h8ee4bcc_1.")
+  var image: String = "quay.io/biocontainers/samtools:1.9--h8ee4bcc_1"
 
   @Args4jOption(required = false, name = "-sudo", usage = "Run via sudo.")
   var sudo: Boolean = false
diff --git a/core/src/main/scala/org/bdgenomics/cannoli/SnpEff.scala b/core/src/main/scala/org/bdgenomics/cannoli/SnpEff.scala
index e3fa9bf..5bf7391 100644
--- a/core/src/main/scala/org/bdgenomics/cannoli/SnpEff.scala
+++ b/core/src/main/scala/org/bdgenomics/cannoli/SnpEff.scala
@@ -40,8 +40,8 @@ class SnpEffArgs extends Args4jBase {
   @Args4jOption(required = false, name = "-executable", usage = "Path to the SnpEff executable. Defaults to snpEff.")
   var executable: String = "snpEff"
 
-  @Args4jOption(required = false, name = "-image", usage = "Container image to use. Defaults to quay.io/biocontainers/snpeff:4.3.1t--0.")
-  var image: String = "quay.io/biocontainers/snpeff:4.3.1t--0"
+  @Args4jOption(required = false, name = "-image", usage = "Container image to use. Defaults to quay.io/biocontainers/snpeff:4.3.1t--1.")
+  var image: String = "quay.io/biocontainers/snpeff:4.3.1t--1"
 
   @Args4jOption(required = false, name = "-sudo", usage = "Run via sudo.")
   var sudo: Boolean = false
diff --git a/core/src/main/scala/org/bdgenomics/cannoli/Vep.scala b/core/src/main/scala/org/bdgenomics/cannoli/Vep.scala
index a62472a..e13b816 100644
--- a/core/src/main/scala/org/bdgenomics/cannoli/Vep.scala
+++ b/core/src/main/scala/org/bdgenomics/cannoli/Vep.scala
@@ -40,8 +40,8 @@ class VepArgs extends Args4jBase {
   @Args4jOption(required = false, name = "-executable", usage = "Path to the Ensembl VEP executable. Defaults to vep.")
   var executable: String = "vep"
 
-  @Args4jOption(required = false, name = "-image", usage = "Container image to use. Defaults to quay.io/biocontainers/ensembl-vep:91.3--htslib1.7_1.")
-  var image: String = "quay.io/biocontainers/ensembl-vep:91.3--htslib1.7_1"
+  @Args4jOption(required = false, name = "-image", usage = "Container image to use. Defaults to quay.io/biocontainers/ensembl-vep:94.0--pl526ha4d7672_0.")
+  var image: String = "quay.io/biocontainers/ensembl-vep:94.0--pl526ha4d7672_0"
 
   @Args4jOption(required = false, name = "-sudo", usage = "Run via sudo.")
   var sudo: Boolean = false