Update container images for bcftools, bedtools, blast, bowtie, bowtie…

…2, bwa, bwa-mem2, minimap2, samtools, snpeff, star, unimap, vep, and vt

core/src/main/scala/org/bdgenomics/cannoli/BcftoolsCall.scala

@@ -35,8 +35,8 @@ class BcftoolsCallArgs extends Args4jBase {
   @Args4jOption(required = false, name = "-executable", usage = "Path to the bcftools executable. Defaults to bcftools.")
   var executable: String = "bcftools"
 
-  @Args4jOption(required = false, name = "-docker_image", usage = "Container image to use. Defaults to quay.io/biocontainers/bcftools:1.20--h8b25389_0.")
-  var image: String = "quay.io/biocontainers/bcftools:1.20--h8b25389_0"
+  @Args4jOption(required = false, name = "-docker_image", usage = "Container image to use. Defaults to quay.io/biocontainers/bcftools:1.21--h8b25389_0.")
+  var image: String = "quay.io/biocontainers/bcftools:1.21--h8b25389_0"
 
   @Args4jOption(required = false, name = "-sudo", usage = "Run via sudo.")
   var sudo: Boolean = false

core/src/main/scala/org/bdgenomics/cannoli/BcftoolsMpileup.scala

@@ -36,8 +36,8 @@ class BcftoolsMpileupArgs extends Args4jBase {
   @Args4jOption(required = false, name = "-executable", usage = "Path to the bcftools executable. Defaults to bcftools.")
   var executable: String = "bcftools"
 
-  @Args4jOption(required = false, name = "-docker_image", usage = "Container image to use. Defaults to quay.io/biocontainers/bcftools:1.20--h8b25389_0.")
-  var image: String = "quay.io/biocontainers/bcftools:1.20--h8b25389_0"
+  @Args4jOption(required = false, name = "-docker_image", usage = "Container image to use. Defaults to quay.io/biocontainers/bcftools:1.21--h8b25389_0.")
+  var image: String = "quay.io/biocontainers/bcftools:1.21--h8b25389_0"
 
   @Args4jOption(required = false, name = "-sudo", usage = "Run via sudo.")
   var sudo: Boolean = false

core/src/main/scala/org/bdgenomics/cannoli/BcftoolsNorm.scala

@@ -39,8 +39,8 @@ 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:1.20--h8b25389_0.")
-  var image: String = "quay.io/biocontainers/bcftools:1.20--h8b25389_0"
+  @Args4jOption(required = false, name = "-image", usage = "Container image to use. Defaults to quay.io/biocontainers/bcftools:1.21--h8b25389_0.")
+  var image: String = "quay.io/biocontainers/bcftools:1.21--h8b25389_0"
 
   @Args4jOption(required = false, name = "-sudo", usage = "Run via sudo.")
   var sudo: Boolean = false

core/src/main/scala/org/bdgenomics/cannoli/BedtoolsIntersect.scala

@@ -47,8 +47,8 @@ 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:2.31.1--hf5e1c6e_0.")
-  var image: String = "quay.io/biocontainers/bedtools:2.31.1--hf5e1c6e_0"
+  @Args4jOption(required = false, name = "-image", usage = "Container image to use. Defaults to quay.io/biocontainers/bedtools:2.31.1--hf5e1c6e_2.")
+  var image: String = "quay.io/biocontainers/bedtools:2.31.1--hf5e1c6e_2"
 
   @Args4jOption(required = false, name = "-sudo", usage = "Run via sudo.")
   var sudo: Boolean = false

core/src/main/scala/org/bdgenomics/cannoli/Blastn.scala

@@ -37,8 +37,8 @@ class BlastnArgs extends Args4jBase {
   @Args4jOption(required = false, name = "-executable", usage = "Path to the blastn executable. Defaults to blastn.")
   var executable: String = "blastn"
 
-  @Args4jOption(required = false, name = "-image", usage = "Container image to use. Defaults to quay.io/biocontainers/blast:2.15.0--pl5321h6f7f691_0.")
-  var image: String = "quay.io/biocontainers/blast:2.15.0--pl5321h6f7f691_0"
+  @Args4jOption(required = false, name = "-image", usage = "Container image to use. Defaults to quay.io/biocontainers/blast:2.16.0--hc155240_2")
+  var image: String = "quay.io/biocontainers/blast:2.16.0--hc155240_2"
 
   @Args4jOption(required = false, name = "-sudo", usage = "Run via sudo.")
   var sudo: Boolean = false

core/src/main/scala/org/bdgenomics/cannoli/Bowtie.scala

@@ -35,8 +35,8 @@ 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:1.3.1--py310h4070885_4.")
-  var image: String = "quay.io/biocontainers/bowtie:1.3.1--py310h4070885_4"
+  @Args4jOption(required = false, name = "-image", usage = "Container image to use. Defaults to quay.io/biocontainers/bowtie:1.3.1--py311h73fc1d6_9.")
+  var image: String = "quay.io/biocontainers/bowtie:1.3.1--py311h73fc1d6_9"
 
   @Args4jOption(required = false, name = "-sudo", usage = "Run via sudo.")
   var sudo: Boolean = false

core/src/main/scala/org/bdgenomics/cannoli/Bowtie2.scala

@@ -36,8 +36,8 @@ class Bowtie2Args extends Args4jBase {
   @Args4jOption(required = false, name = "-executable", usage = "Path to the Bowtie 2 executable. Defaults to bowtie2.")
   var executable: String = "bowtie2"
 
-  @Args4jOption(required = false, name = "-image", usage = "Container image to use. Defaults to quay.io/biocontainers/bowtie2:2.5.2--py39h6fed5c7_0.")
-  var image: String = "quay.io/biocontainers/bowtie2:2.5.2--py39h6fed5c7_0"
+  @Args4jOption(required = false, name = "-image", usage = "Container image to use. Defaults to quay.io/biocontainers/bowtie2:2.5.4--h7071971_4.")
+  var image: String = "quay.io/biocontainers/bowtie2:2.5.4--h7071971_4"
 
   @Args4jOption(required = false, name = "-sudo", usage = "Run via sudo.")
   var sudo: Boolean = false

core/src/main/scala/org/bdgenomics/cannoli/BwaMem.scala

@@ -38,8 +38,8 @@ class BwaMemArgs extends ReadGroupArgs {
   @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:0.7.18--he4a0461_0.")
-  var image: String = "quay.io/biocontainers/bwa:0.7.18--he4a0461_0"
+  @Args4jOption(required = false, name = "-image", usage = "Container image to use. Defaults to quay.io/biocontainers/bwa:0.7.18--he4a0461_1.")
+  var image: String = "quay.io/biocontainers/bwa:0.7.18--he4a0461_1"
 
   @Args4jOption(required = false, name = "-sudo", usage = "Run via sudo.")
   var sudo: Boolean = false

core/src/main/scala/org/bdgenomics/cannoli/BwaMem2.scala

@@ -38,8 +38,8 @@ class BwaMem2Args extends ReadGroupArgs {
   @Args4jOption(required = false, name = "-executable", usage = "Path to the Bwa-mem2 executable. Defaults to bwa-mem2.")
   var executable: String = "bwa-mem2"
 
-  @Args4jOption(required = false, name = "-image", usage = "Container image to use. Defaults to quay.io/biocontainers/bwa-mem2:2.2.1--hd03093a_2.")
-  var image: String = "quay.io/biocontainers/bwa-mem2:2.2.1--hd03093a_2"
+  @Args4jOption(required = false, name = "-image", usage = "Container image to use. Defaults to quay.io/biocontainers/bwa-mem2:2.2.1--hd03093a_5.")
+  var image: String = "quay.io/biocontainers/bwa-mem2:2.2.1--hd03093a_5"
 
   @Args4jOption(required = false, name = "-sudo", usage = "Run via sudo.")
   var sudo: Boolean = false

core/src/main/scala/org/bdgenomics/cannoli/Minimap2.scala

@@ -36,8 +36,8 @@ class Minimap2Args extends ReadGroupArgs {
   @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/minimap2:2.27--he4a0461_1.")
-  var image: String = "quay.io/biocontainers/minimap2:2.27--he4a0461_1"
+  @Args4jOption(required = false, name = "-image", usage = "Container image to use. Defaults to quay.io/biocontainers/minimap2:2.28--he4a0461_3.")
+  var image: String = "quay.io/biocontainers/minimap2:2.28--he4a0461_3"
 
   @Args4jOption(required = false, name = "-sudo", usage = "Run via sudo.")
   var sudo: Boolean = false

core/src/main/scala/org/bdgenomics/cannoli/SamtoolsMpileup.scala

@@ -36,8 +36,8 @@ 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:1.20--h50ea8bc_0.")
-  var image: String = "quay.io/biocontainers/samtools:1.20--h50ea8bc_0"
+  @Args4jOption(required = false, name = "-docker_image", usage = "Container image to use. Defaults to quay.io/biocontainers/samtools:1.21--h50ea8bc_0.")
+  var image: String = "quay.io/biocontainers/samtools:1.21--h50ea8bc_0"
 
   @Args4jOption(required = false, name = "-sudo", usage = "Run via sudo.")
   var sudo: Boolean = false

core/src/main/scala/org/bdgenomics/cannoli/SingleEndBowtie2.scala

@@ -39,8 +39,8 @@ class SingleEndBowtie2Args extends Args4jBase {
   @Args4jOption(required = false, name = "-executable", usage = "Path to the Bowtie 2 executable. Defaults to bowtie2.")
   var executable: String = "bowtie2"
 
-  @Args4jOption(required = false, name = "-image", usage = "Container image to use. Defaults to quay.io/biocontainers/bowtie2:2.5.2--py39h6fed5c7_0.")
-  var image: String = "quay.io/biocontainers/bowtie2:2.5.2--py39h6fed5c7_0"
+  @Args4jOption(required = false, name = "-image", usage = "Container image to use. Defaults to quay.io/biocontainers/bowtie2:2.5.2--2.5.4--h7071971_4.")
+  var image: String = "quay.io/biocontainers/bowtie2:2.5.4--h7071971_4"
 
   @Args4jOption(required = false, name = "-sudo", usage = "Run via sudo.")
   var sudo: Boolean = false

core/src/main/scala/org/bdgenomics/cannoli/SingleEndStar.scala

@@ -34,8 +34,8 @@ class SingleEndStarArgs extends Args4jBase {
   @Args4jOption(required = false, name = "-executable", usage = "Path to the STAR-Mapper executable. Defaults to STAR.")
   var executable: String = "STAR"
 
-  @Args4jOption(required = false, name = "-image", usage = "Container image to use. Defaults to quay.io/biocontainers/star:2.7.10a--h9ee0642_0.")
-  var image: String = "quay.io/biocontainers/star:2.7.10a--h9ee0642_0"
+  @Args4jOption(required = false, name = "-image", usage = "Container image to use. Defaults to quay.io/biocontainers/star:2.7.11b--h43eeafb_2.")
+  var image: String = "quay.io/biocontainers/star:2.7.11b--h43eeafb_2"
 
   @Args4jOption(required = false, name = "-sudo", usage = "Run via sudo.")
   var sudo: Boolean = false

core/src/main/scala/org/bdgenomics/cannoli/SnpEff.scala

@@ -39,8 +39,8 @@ 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:5.1d--hdfd78af_0.")
-  var image: String = "quay.io/biocontainers/snpeff:5.1d--hdfd78af_0"
+  @Args4jOption(required = false, name = "-image", usage = "Container image to use. Defaults to quay.io/biocontainers/snpeff:5.2--hdfd78af_1.")
+  var image: String = "quay.io/biocontainers/snpeff:5.2--hdfd78af_1"
 
   @Args4jOption(required = false, name = "-sudo", usage = "Run via sudo.")
   var sudo: Boolean = false

core/src/main/scala/org/bdgenomics/cannoli/Star.scala

@@ -35,8 +35,8 @@ class StarArgs extends Args4jBase {
   @Args4jOption(required = false, name = "-executable", usage = "Path to the STAR-Mapper executable. Defaults to STAR.")
   var executable: String = "STAR"
 
-  @Args4jOption(required = false, name = "-image", usage = "Container image to use. Defaults to quay.io/biocontainers/star:2.7.10b--h9ee0642_0.")
-  var image: String = "quay.io/biocontainers/star:2.7.10b--h9ee0642_0"
+  @Args4jOption(required = false, name = "-image", usage = "Container image to use. Defaults to quay.io/biocontainers/star:2.7.11b--h43eeafb_2.")
+  var image: String = "quay.io/biocontainers/star:2.7.11b--h43eeafb_2"
 
   @Args4jOption(required = false, name = "-sudo", usage = "Run via sudo.")
   var sudo: Boolean = false

core/src/main/scala/org/bdgenomics/cannoli/Unimap.scala

@@ -36,8 +36,8 @@ class UnimapArgs extends ReadGroupArgs {
   @Args4jOption(required = false, name = "-executable", usage = "Path to the Unimap executable. Defaults to unimap.")
   var executable: String = "unimap"
 
-  @Args4jOption(required = false, name = "-image", usage = "Container image to use. Defaults to quay.io/biocontainers/unimap:0.1--h7132678_2.")
-  var image: String = "quay.io/biocontainers/unimap:0.1--h7132678_2"
+  @Args4jOption(required = false, name = "-image", usage = "Container image to use. Defaults to quay.io/biocontainers/unimap:0.1--he4a0461_4.")
+  var image: String = "quay.io/biocontainers/unimap:0.1--he4a0461_4"
 
   @Args4jOption(required = false, name = "-sudo", usage = "Run via sudo.")
   var sudo: Boolean = false

core/src/main/scala/org/bdgenomics/cannoli/Vep.scala

@@ -39,8 +39,8 @@ 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:108.2--pl5321h4a94de4_0.")
-  var image: String = "quay.io/biocontainers/ensembl-vep:108.2--pl5321h4a94de4_0"
+  @Args4jOption(required = false, name = "-image", usage = "Container image to use. Defaults to quay.io/biocontainers/ensembl-vep:113.0--pl5321h2a3209d_0.")
+  var image: String = "quay.io/biocontainers/ensembl-vep:113.0--pl5321h2a3209d_0"
 
   @Args4jOption(required = false, name = "-sudo", usage = "Run via sudo.")
   var sudo: Boolean = false

core/src/main/scala/org/bdgenomics/cannoli/VtNormalize.scala

@@ -39,8 +39,8 @@ class VtNormalizeArgs extends Args4jBase {
   @Args4jOption(required = false, name = "-executable", usage = "Path to the vt executable. Defaults to vt.")
   var executable: String = "vt"
 
-  @Args4jOption(required = false, name = "-image", usage = "Container image to use. Defaults to quay.io/biocontainers/vt:0.57721--h5eb663c_7.")
-  var image: String = "quay.io/biocontainers/vt:0.57721--h5eb663c_7"
+  @Args4jOption(required = false, name = "-image", usage = "Container image to use. Defaults to quay.io/biocontainers/vt:0.57721--hf74b74d_1.")
+  var image: String = "quay.io/biocontainers/vt:0.57721--hf74b74d_1"
 
   @Args4jOption(required = false, name = "-sudo", usage = "Run via sudo.")
   var sudo: Boolean = false