From ef5b0dd977d19cbd2a233bb0783cd02aaedc208b Mon Sep 17 00:00:00 2001 From: Rike Date: Thu, 9 Jun 2022 14:54:19 +0200 Subject: [PATCH 1/8] gatk4 version update to 4.2.6.1 --- modules/gatk4/markduplicatesspark/main.nf | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/modules/gatk4/markduplicatesspark/main.nf b/modules/gatk4/markduplicatesspark/main.nf index db6a1aa1..0bafe7ce 100644 --- a/modules/gatk4/markduplicatesspark/main.nf +++ b/modules/gatk4/markduplicatesspark/main.nf @@ -2,10 +2,10 @@ process GATK4_MARKDUPLICATES_SPARK { tag "$meta.id" label 'process_high' - conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0 conda-forge::openjdk=8.0.312" : null) + conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1 conda-forge::openjdk=8.0.312" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0' : - 'broadinstitute/gatk:4.2.3.0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': + 'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }" input: tuple val(meta), path(bam) From b9e397ff15a98c8b70099579f7645a32c467d65b Mon Sep 17 00:00:00 2001 From: Rike Date: Thu, 9 Jun 2022 15:06:46 +0200 Subject: [PATCH 2/8] use broadinstitute container --- modules/gatk4/markduplicatesspark/main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/gatk4/markduplicatesspark/main.nf b/modules/gatk4/markduplicatesspark/main.nf index 0bafe7ce..9f77821e 100644 --- a/modules/gatk4/markduplicatesspark/main.nf +++ b/modules/gatk4/markduplicatesspark/main.nf @@ -5,7 +5,7 @@ process GATK4_MARKDUPLICATES_SPARK { conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1 conda-forge::openjdk=8.0.312" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': - 'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }" + 'broadinstitute/gatk4:4.2.6.1' }" input: tuple val(meta), path(bam) From 89a6a03e38b8b5869a2e1e5abfe4b4cc4938c622 Mon Sep 17 00:00:00 2001 From: Rike Date: Thu, 9 Jun 2022 15:09:19 +0200 Subject: [PATCH 3/8] fix container tag --- modules/gatk4/markduplicatesspark/main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/gatk4/markduplicatesspark/main.nf b/modules/gatk4/markduplicatesspark/main.nf index 9f77821e..52faf5bc 100644 --- a/modules/gatk4/markduplicatesspark/main.nf +++ b/modules/gatk4/markduplicatesspark/main.nf @@ -5,7 +5,7 @@ process GATK4_MARKDUPLICATES_SPARK { conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1 conda-forge::openjdk=8.0.312" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': - 'broadinstitute/gatk4:4.2.6.1' }" + 'broadinstitute/gatk:4.2.6.1' }" input: tuple val(meta), path(bam) From 8e8f4c9c51a7b229dd45e9b287d48115c238baf3 Mon Sep 17 00:00:00 2001 From: Rike Date: Thu, 9 Jun 2022 15:16:11 +0200 Subject: [PATCH 4/8] remove singulairty container --- modules/gatk4/markduplicatesspark/main.nf | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/modules/gatk4/markduplicatesspark/main.nf b/modules/gatk4/markduplicatesspark/main.nf index 52faf5bc..b8c315fc 100644 --- a/modules/gatk4/markduplicatesspark/main.nf +++ b/modules/gatk4/markduplicatesspark/main.nf @@ -3,9 +3,7 @@ process GATK4_MARKDUPLICATES_SPARK { label 'process_high' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1 conda-forge::openjdk=8.0.312" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': - 'broadinstitute/gatk:4.2.6.1' }" + container 'broadinstitute/gatk:4.2.6.1' input: tuple val(meta), path(bam) From 6a4732ef3b76b54d75533e6be9ba57e3008d4853 Mon Sep 17 00:00:00 2001 From: Rike Date: Thu, 9 Jun 2022 15:29:00 +0200 Subject: [PATCH 5/8] similar issues arise with bqsrspark, also use broadinstitute container --- modules/gatk4/applybqsrspark/main.nf | 6 ++---- modules/gatk4/baserecalibratorspark/main.nf | 6 ++---- 2 files changed, 4 insertions(+), 8 deletions(-) diff --git a/modules/gatk4/applybqsrspark/main.nf b/modules/gatk4/applybqsrspark/main.nf index 9d7891ba..5890278a 100644 --- a/modules/gatk4/applybqsrspark/main.nf +++ b/modules/gatk4/applybqsrspark/main.nf @@ -2,10 +2,8 @@ process GATK4_APPLYBQSR_SPARK { tag "$meta.id" label 'process_low' - conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': - 'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }" + conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1 conda-forge::openjdk=8.0.312" : null) + container 'broadinstitute/gatk:4.2.6.1' input: tuple val(meta), path(input), path(input_index), path(bqsr_table), path(intervals) diff --git a/modules/gatk4/baserecalibratorspark/main.nf b/modules/gatk4/baserecalibratorspark/main.nf index 79988b72..755122cb 100644 --- a/modules/gatk4/baserecalibratorspark/main.nf +++ b/modules/gatk4/baserecalibratorspark/main.nf @@ -2,10 +2,8 @@ process GATK4_BASERECALIBRATOR_SPARK { tag "$meta.id" label 'process_low' - conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': - 'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }" + conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1 conda-forge::openjdk=8.0.312" : null) + container 'broadinstitute/gatk:4.2.6.1' input: tuple val(meta), path(input), path(input_index), path(intervals) From 95633c6853c3a33a7cf65720381874582cd3b7c8 Mon Sep 17 00:00:00 2001 From: Rike Date: Thu, 9 Jun 2022 15:30:47 +0200 Subject: [PATCH 6/8] update checksum --- tests/modules/gatk4/markduplicatesspark/test.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/modules/gatk4/markduplicatesspark/test.yml b/tests/modules/gatk4/markduplicatesspark/test.yml index 4ef9b916..1ef7f543 100644 --- a/tests/modules/gatk4/markduplicatesspark/test.yml +++ b/tests/modules/gatk4/markduplicatesspark/test.yml @@ -5,7 +5,7 @@ - gatk4/markduplicatesspark files: - path: output/gatk4/test.bam - md5sum: dc1a09ac6371aab7c50d1a554baa06d3 + md5sum: 4b5abb065d498bece619f9bd4cc929e1 - path: output/gatk4/versions.yml - name: gatk4 markduplicatesspark test_gatk4_markduplicates_spark_multiple_bams From a5583143c46e2b7b56b513e61141a36b5c0e29d3 Mon Sep 17 00:00:00 2001 From: Rike Date: Thu, 9 Jun 2022 15:38:28 +0200 Subject: [PATCH 7/8] update checksum --- tests/modules/gatk4/applybqsrspark/test.yml | 2 +- tests/modules/gatk4/markduplicatesspark/test.yml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/tests/modules/gatk4/applybqsrspark/test.yml b/tests/modules/gatk4/applybqsrspark/test.yml index 1e4f8b47..5a1c3df6 100644 --- a/tests/modules/gatk4/applybqsrspark/test.yml +++ b/tests/modules/gatk4/applybqsrspark/test.yml @@ -15,7 +15,7 @@ - gatk4/applybqsrspark files: - path: output/gatk4/test.bam - md5sum: 2ca2446f0125890280056fd7da822732 + md5sum: db27196dbd626edb0509aac4589dedcf - path: output/gatk4/versions.yml - name: gatk4 applybqsr test_gatk4_applybqsr_spark_cram diff --git a/tests/modules/gatk4/markduplicatesspark/test.yml b/tests/modules/gatk4/markduplicatesspark/test.yml index 1ef7f543..4ef9b916 100644 --- a/tests/modules/gatk4/markduplicatesspark/test.yml +++ b/tests/modules/gatk4/markduplicatesspark/test.yml @@ -5,7 +5,7 @@ - gatk4/markduplicatesspark files: - path: output/gatk4/test.bam - md5sum: 4b5abb065d498bece619f9bd4cc929e1 + md5sum: dc1a09ac6371aab7c50d1a554baa06d3 - path: output/gatk4/versions.yml - name: gatk4 markduplicatesspark test_gatk4_markduplicates_spark_multiple_bams From 30262d1fdd032df12c2dedca55099d8eaaf7b136 Mon Sep 17 00:00:00 2001 From: Rike Date: Thu, 9 Jun 2022 15:44:12 +0200 Subject: [PATCH 8/8] remove variable checksum --- tests/modules/gatk4/applybqsrspark/test.yml | 1 - 1 file changed, 1 deletion(-) diff --git a/tests/modules/gatk4/applybqsrspark/test.yml b/tests/modules/gatk4/applybqsrspark/test.yml index 5a1c3df6..b7b8c72d 100644 --- a/tests/modules/gatk4/applybqsrspark/test.yml +++ b/tests/modules/gatk4/applybqsrspark/test.yml @@ -15,7 +15,6 @@ - gatk4/applybqsrspark files: - path: output/gatk4/test.bam - md5sum: db27196dbd626edb0509aac4589dedcf - path: output/gatk4/versions.yml - name: gatk4 applybqsr test_gatk4_applybqsr_spark_cram