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Update default container image versions.
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@heuermh
heuermh committed Jan 24, 2022
1 parent 4cceff9 commit 5085654
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Showing 14 changed files with 28 additions and 28 deletions.
4 changes: 2 additions & 2 deletions core/src/main/scala/org/bdgenomics/cannoli/BcftoolsCall.scala
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Expand Up @@ -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:1.14--h88f3f91_0.")
var image: String = "quay.io/biocontainers/bcftools:1.14--h88f3f91_0"
@Args4jOption(required = false, name = "-docker_image", usage = "Container image to use. Defaults to quay.io/biocontainers/bcftools:1.14--hde04aa1_1.")
var image: String = "quay.io/biocontainers/bcftools:1.14--hde04aa1_1"

@Args4jOption(required = false, name = "-sudo", usage = "Run via sudo.")
var sudo: Boolean = false
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4 changes: 2 additions & 2 deletions core/src/main/scala/org/bdgenomics/cannoli/BcftoolsMpileup.scala
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Expand Up @@ -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:1.14--h88f3f91_0.")
var image: String = "quay.io/biocontainers/bcftools:1.14--h88f3f91_0"
@Args4jOption(required = false, name = "-docker_image", usage = "Container image to use. Defaults to quay.io/biocontainers/bcftools:1.14--hde04aa1_1.")
var image: String = "quay.io/biocontainers/bcftools:1.14--hde04aa1_1"

@Args4jOption(required = false, name = "-sudo", usage = "Run via sudo.")
var sudo: Boolean = false
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4 changes: 2 additions & 2 deletions core/src/main/scala/org/bdgenomics/cannoli/BcftoolsNorm.scala
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Expand Up @@ -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:1.14--h88f3f91_0.")
var image: String = "quay.io/biocontainers/bcftools:1.14--h88f3f91_0"
@Args4jOption(required = false, name = "-image", usage = "Container image to use. Defaults to quay.io/biocontainers/bcftools:1.14--hde04aa1_1.")
var image: String = "quay.io/biocontainers/bcftools:1.14--hde04aa1_1"

@Args4jOption(required = false, name = "-sudo", usage = "Run via sudo.")
var sudo: Boolean = false
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4 changes: 2 additions & 2 deletions core/src/main/scala/org/bdgenomics/cannoli/BedtoolsIntersect.scala
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Expand Up @@ -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:2.30.0--hc088bd4_0.")
var image: String = "quay.io/biocontainers/bedtools:2.30.0--hc088bd4_0"
@Args4jOption(required = false, name = "-image", usage = "Container image to use. Defaults to quay.io/biocontainers/bedtools:2.30.0--h7d7f7ad_2.")
var image: String = "quay.io/biocontainers/bedtools:2.30.0--h7d7f7ad_2"

@Args4jOption(required = false, name = "-sudo", usage = "Run via sudo.")
var sudo: Boolean = false
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4 changes: 2 additions & 2 deletions core/src/main/scala/org/bdgenomics/cannoli/Blastn.scala
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Expand Up @@ -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:2.11.0--pl526he19e7b1_0.")
var image: String = "quay.io/biocontainers/blast:2.11.0--pl526he19e7b1_0"
@Args4jOption(required = false, name = "-image", usage = "Container image to use. Defaults to quay.io/biocontainers/blast:2.12.0--pl5262h3289130_0.")
var image: String = "quay.io/biocontainers/blast:2.12.0--pl5262h3289130_0"

@Args4jOption(required = false, name = "-sudo", usage = "Run via sudo.")
var sudo: Boolean = false
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4 changes: 2 additions & 2 deletions core/src/main/scala/org/bdgenomics/cannoli/Bowtie.scala
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Expand Up @@ -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--py39h176da8b_0.")
var image: String = "quay.io/biocontainers/bowtie:1.3.1--py39h176da8b_0"
@Args4jOption(required = false, name = "-image", usage = "Container image to use. Defaults to quay.io/biocontainers/bowtie:1.3.1--py38hcf49a77_0.")
var image: String = "quay.io/biocontainers/bowtie:1.3.1--py38hcf49a77_0"

@Args4jOption(required = false, name = "-sudo", usage = "Run via sudo.")
var sudo: Boolean = false
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4 changes: 2 additions & 2 deletions core/src/main/scala/org/bdgenomics/cannoli/BwaMem.scala
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Expand Up @@ -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:0.7.17--hed695b0_7.")
var image: String = "quay.io/biocontainers/bwa:0.7.17--hed695b0_7"
@Args4jOption(required = false, name = "-image", usage = "Container image to use. Defaults to quay.io/biocontainers/bwa:0.7.17--h5bf99c6_8.")
var image: String = "quay.io/biocontainers/bwa:0.7.17--h5bf99c6_8"

@Args4jOption(required = false, name = "-sudo", usage = "Run via sudo.")
var sudo: Boolean = false
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4 changes: 2 additions & 2 deletions core/src/main/scala/org/bdgenomics/cannoli/BwaMem2.scala
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Expand Up @@ -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--he513fc3_0.")
var image: String = "quay.io/biocontainers/bwa-mem2:2.2.1--he513fc3_0"
@Args4jOption(required = false, name = "-image", usage = "Container image to use. Defaults to quay.io/biocontainers/bwa-mem2:2.2.1--h9a82719_1.")
var image: String = "quay.io/biocontainers/bwa-mem2:2.2.1--h9a82719_1"

@Args4jOption(required = false, name = "-sudo", usage = "Run via sudo.")
var sudo: Boolean = false
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4 changes: 2 additions & 2 deletions core/src/main/scala/org/bdgenomics/cannoli/Freebayes.scala
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Expand Up @@ -36,8 +36,8 @@ 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:1.3.5--py38hcc087cc_2.")
var image: String = "quay.io/biocontainers/freebayes:1.3.5--py38hcc087cc_2"
@Args4jOption(required = false, name = "-image", usage = "Container image to use. Defaults to quay.io/biocontainers/freebayes:1.3.5--py38h8367b0b_4.")
var image: String = "quay.io/biocontainers/freebayes:1.3.5--py38h8367b0b_4"

@Args4jOption(required = false, name = "-sudo", usage = "Run via sudo.")
var sudo: Boolean = false
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4 changes: 2 additions & 2 deletions core/src/main/scala/org/bdgenomics/cannoli/MagicBlast.scala
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Expand Up @@ -37,8 +37,8 @@ class MagicBlastArgs extends Args4jBase {
@Args4jOption(required = false, name = "-executable", usage = "Path to the Magic-BLAST executable. Defaults to magicblast.")
var executable: String = "magicblast"

@Args4jOption(required = false, name = "-image", usage = "Container image to use. Defaults to quay.io/biocontainers/magicblast:1.5.0--h2d02072_0.")
var image: String = "quay.io/biocontainers/magicblast:1.5.0--h2d02072_0"
@Args4jOption(required = false, name = "-image", usage = "Container image to use. Defaults to quay.io/biocontainers/magicblast:1.6.0--h95f258a_0.")
var image: String = "quay.io/biocontainers/magicblast:1.6.0--h95f258a_0"

@Args4jOption(required = false, name = "-sudo", usage = "Run via sudo.")
var sudo: Boolean = false
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4 changes: 2 additions & 2 deletions core/src/main/scala/org/bdgenomics/cannoli/Minimap2.scala
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Expand Up @@ -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/minimap2:2.22--h5bf99c6_0.")
var image: String = "quay.io/biocontainers/minimap2:2.22--h5bf99c6_0"
@Args4jOption(required = false, name = "-image", usage = "Container image to use. Defaults to quay.io/biocontainers/minimap2:2.24--h5bf99c6_0.")
var image: String = "quay.io/biocontainers/minimap2:2.24--h5bf99c6_0"

@Args4jOption(required = false, name = "-sudo", usage = "Run via sudo.")
var sudo: Boolean = false
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4 changes: 2 additions & 2 deletions core/src/main/scala/org/bdgenomics/cannoli/Star.scala
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Expand Up @@ -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:2.7.9a--h9ee0642_0.")
var image: String = "quay.io/biocontainers/star:2.7.9a--h9ee0642_0"
@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 = "-sudo", usage = "Run via sudo.")
var sudo: Boolean = false
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4 changes: 2 additions & 2 deletions core/src/main/scala/org/bdgenomics/cannoli/Vep.scala
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Expand Up @@ -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:103.1--pl526hecda079_0.")
var image: String = "quay.io/biocontainers/ensembl-vep:103.1--pl526hecda079_0"
@Args4jOption(required = false, name = "-image", usage = "Container image to use. Defaults to quay.io/biocontainers/ensembl-vep:105.0--pl5262h4a94de4_0.")
var image: String = "quay.io/biocontainers/ensembl-vep:105.0--pl5262h4a94de4_0"

@Args4jOption(required = false, name = "-sudo", usage = "Run via sudo.")
var sudo: Boolean = false
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4 changes: 2 additions & 2 deletions core/src/main/scala/org/bdgenomics/cannoli/VtNormalize.scala
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Expand Up @@ -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--h41af197_4.")
var image: String = "quay.io/biocontainers/vt:0.57721--h41af197_4"
@Args4jOption(required = false, name = "-image", usage = "Container image to use. Defaults to quay.io/biocontainers/vt:0.57721--hf1e2573_5.")
var image: String = "quay.io/biocontainers/vt:0.57721--hf1e2573_5"

@Args4jOption(required = false, name = "-sudo", usage = "Run via sudo.")
var sudo: Boolean = false
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