From 44bb35fd4319c35b3dd1b2aa8df169d5eb288e7e Mon Sep 17 00:00:00 2001 From: Michael L Heuer Date: Wed, 19 Oct 2022 11:34:31 -0500 Subject: [PATCH 1/2] Update bcftools container image to 1.16--hfe4b78e_1. --- core/src/main/scala/org/bdgenomics/cannoli/BcftoolsCall.scala | 4 ++-- .../main/scala/org/bdgenomics/cannoli/BcftoolsMpileup.scala | 4 ++-- core/src/main/scala/org/bdgenomics/cannoli/BcftoolsNorm.scala | 4 ++-- 3 files changed, 6 insertions(+), 6 deletions(-) diff --git a/core/src/main/scala/org/bdgenomics/cannoli/BcftoolsCall.scala b/core/src/main/scala/org/bdgenomics/cannoli/BcftoolsCall.scala index 37aefff..c15719b 100644 --- a/core/src/main/scala/org/bdgenomics/cannoli/BcftoolsCall.scala +++ b/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:1.15.1--h0ea216a_0.") - var image: String = "quay.io/biocontainers/bcftools:1.15.1--h0ea216a_0" + @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 = "-sudo", usage = "Run via sudo.") var sudo: Boolean = false diff --git a/core/src/main/scala/org/bdgenomics/cannoli/BcftoolsMpileup.scala b/core/src/main/scala/org/bdgenomics/cannoli/BcftoolsMpileup.scala index 7853abb..a651ae3 100644 --- a/core/src/main/scala/org/bdgenomics/cannoli/BcftoolsMpileup.scala +++ b/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:1.15.1--h0ea216a_0.") - var image: String = "quay.io/biocontainers/bcftools:1.15.1--h0ea216a_0" + @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 = "-sudo", usage = "Run via sudo.") var sudo: Boolean = false diff --git a/core/src/main/scala/org/bdgenomics/cannoli/BcftoolsNorm.scala b/core/src/main/scala/org/bdgenomics/cannoli/BcftoolsNorm.scala index 70f4c16..002c3bf 100644 --- a/core/src/main/scala/org/bdgenomics/cannoli/BcftoolsNorm.scala +++ b/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:1.15.1--h0ea216a_0.") - var image: String = "quay.io/biocontainers/bcftools:1.15.1--h0ea216a_0" + @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 = "-sudo", usage = "Run via sudo.") var sudo: Boolean = false From 27fef799498ca3c400c860fd81ccc5e5fc4455ca Mon Sep 17 00:00:00 2001 From: Michael L Heuer Date: Wed, 19 Oct 2022 11:34:56 -0500 Subject: [PATCH 2/2] Update samtools container image to 1.16.1--h6899075_1. --- .../main/scala/org/bdgenomics/cannoli/SamtoolsMpileup.scala | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/core/src/main/scala/org/bdgenomics/cannoli/SamtoolsMpileup.scala b/core/src/main/scala/org/bdgenomics/cannoli/SamtoolsMpileup.scala index 2b558aa..b9ce1a3 100644 --- a/core/src/main/scala/org/bdgenomics/cannoli/SamtoolsMpileup.scala +++ b/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:1.15.1--h1170115_0.") - var image: String = "quay.io/biocontainers/samtools:1.15.1--h1170115_0" + @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 = "-sudo", usage = "Run via sudo.") var sudo: Boolean = false