From f6524fefc0a217f7ec14af1c048126f44a383977 Mon Sep 17 00:00:00 2001 From: Michael L Heuer Date: Tue, 17 Dec 2019 09:39:41 -0600 Subject: [PATCH] Update docker image tags. --- 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 ++-- .../main/scala/org/bdgenomics/cannoli/BedtoolsIntersect.scala | 4 ++-- .../main/scala/org/bdgenomics/cannoli/SamtoolsMpileup.scala | 4 ++-- 5 files changed, 10 insertions(+), 10 deletions(-) diff --git a/core/src/main/scala/org/bdgenomics/cannoli/BcftoolsCall.scala b/core/src/main/scala/org/bdgenomics/cannoli/BcftoolsCall.scala index 1386788..e03ad9c 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:1.9--h68d8f2e_8.") - var image: String = "quay.io/biocontainers/bcftools:1.9--h68d8f2e_8" + @Args4jOption(required = false, name = "-docker_image", usage = "Container image to use. Defaults to quay.io/biocontainers/bcftools:1.10.1--hd2cd319_0.") + var image: String = "quay.io/biocontainers/bcftools:1.10.1--hd2cd319_0" @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 152eb52..89455e5 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:1.9--h68d8f2e_8.") - var image: String = "quay.io/biocontainers/bcftools:1.9--h68d8f2e_8" + @Args4jOption(required = false, name = "-docker_image", usage = "Container image to use. Defaults to quay.io/biocontainers/bcftools:1.10.1--hd2cd319_0.") + var image: String = "quay.io/biocontainers/bcftools:1.10.1--hd2cd319_0" @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 4e9b536..4ebcebd 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:1.9--h68d8f2e_8.") - var image: String = "quay.io/biocontainers/bcftools:1.9--h68d8f2e_8" + @Args4jOption(required = false, name = "-image", usage = "Container image to use. Defaults to quay.io/biocontainers/bcftools:1.10.1--hd2cd319_0.") + var image: String = "quay.io/biocontainers/bcftools:1.10.1--hd2cd319_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 d922f0b..ad7eae0 100644 --- a/core/src/main/scala/org/bdgenomics/cannoli/BedtoolsIntersect.scala +++ b/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:2.29.0--hc088bd4_3.") - var image: String = "quay.io/biocontainers/bedtools:2.29.0--hc088bd4_3" + @Args4jOption(required = false, name = "-image", usage = "Container image to use. Defaults to quay.io/biocontainers/bedtools:2.29.1--hc088bd4_1.") + var image: String = "quay.io/biocontainers/bedtools:2.29.1--hc088bd4_1" @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 bea304d..b11c81e 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:1.9--h10a08f8_12.") - var image: String = "quay.io/biocontainers/samtools:1.9--h10a08f8_12" + @Args4jOption(required = false, name = "-docker_image", usage = "Container image to use. Defaults to quay.io/biocontainers/samtools:1.10--h9402c20_1.") + var image: String = "quay.io/biocontainers/samtools:1.10--h9402c20_1" @Args4jOption(required = false, name = "-sudo", usage = "Run via sudo.") var sudo: Boolean = false