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Update bcftools and samtools container images to version 1.19 #362

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merged 2 commits into from
Dec 14, 2023
Merged

Update bcftools and samtools container images to version 1.19 #362

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7dbed50
Update bcftools container image to 1.19--h8b25389_0.
heuermh Dec 14, 2023
b2db9ea
Update samtools container image to 1.19--h50ea8bc_0.
heuermh Dec 14, 2023
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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:1.16--hfe4b78e_1.")
var image: String = "quay.io/biocontainers/bcftools:1.16--hfe4b78e_1"
@Args4jOption(required = false, name = "-docker_image", usage = "Container image to use. Defaults to quay.io/biocontainers/bcftools:1.19--h8b25389_0.")
var image: String = "quay.io/biocontainers/bcftools:1.19--h8b25389_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/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:1.16--hfe4b78e_1.")
var image: String = "quay.io/biocontainers/bcftools:1.16--hfe4b78e_1"
@Args4jOption(required = false, name = "-docker_image", usage = "Container image to use. Defaults to quay.io/biocontainers/bcftools:1.19--h8b25389_0.")
var image: String = "quay.io/biocontainers/bcftools:1.19--h8b25389_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/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:1.16--hfe4b78e_1.")
var image: String = "quay.io/biocontainers/bcftools:1.16--hfe4b78e_1"
@Args4jOption(required = false, name = "-image", usage = "Container image to use. Defaults to quay.io/biocontainers/bcftools:1.19--h8b25389_0.")
var image: String = "quay.io/biocontainers/bcftools:1.19--h8b25389_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/SamtoolsMpileup.scala
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Expand Up @@ -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:1.16.1--h6899075_1.")
var image: String = "quay.io/biocontainers/samtools:1.16.1--h6899075_1"
@Args4jOption(required = false, name = "-docker_image", usage = "Container image to use. Defaults to quay.io/biocontainers/samtools:1.19--h50ea8bc_0.")
var image: String = "quay.io/biocontainers/samtools:1.19--h50ea8bc_0"

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