From de6ebf8df05758873ebdd0c315e089d6e93ff29e Mon Sep 17 00:00:00 2001 From: asp8200 Date: Mon, 4 Mar 2024 21:58:30 +0000 Subject: [PATCH 1/2] Using containerOptions for GATK Spark modules --- conf/test.config | 2 +- conf/test/cache.config | 2 +- conf/test/use_gatk_spark.config | 2 -- modules/nf-core/gatk4spark/applybqsr/main.nf | 4 ++++ modules/nf-core/gatk4spark/baserecalibrator/main.nf | 4 ++++ modules/nf-core/gatk4spark/markduplicates/main.nf | 4 ++++ nextflow.config | 2 +- 7 files changed, 15 insertions(+), 5 deletions(-) diff --git a/conf/test.config b/conf/test.config index 002b35d183..f55085c663 100644 --- a/conf/test.config +++ b/conf/test.config @@ -108,7 +108,7 @@ if (System.getenv('PROFILE')) { } else if ("$PROFILE" == "docker") { conda.enabled = false docker.enabled = true - docker.runOptions = { params.use_gatk_spark ? '' : '-u $(id -u):$(id -g)' }.call() + docker.runOptions = '-u $(id -u):$(id -g)' charliecloud.enabled = false podman.enabled = false shifter.enabled = false diff --git a/conf/test/cache.config b/conf/test/cache.config index 5aba7dc0f6..5e5145b6bc 100644 --- a/conf/test/cache.config +++ b/conf/test/cache.config @@ -116,7 +116,7 @@ if (System.getenv('PROFILE')) { } else if ("$PROFILE" == "docker") { conda.enabled = false docker.enabled = true - docker.runOptions = { params.use_gatk_spark ? '' : '-u $(id -u):$(id -g)' }.call() + docker.runOptions = '-u $(id -u):$(id -g)' charliecloud.enabled = false podman.enabled = false shifter.enabled = false diff --git a/conf/test/use_gatk_spark.config b/conf/test/use_gatk_spark.config index 41bbc16452..bd40af1b77 100644 --- a/conf/test/use_gatk_spark.config +++ b/conf/test/use_gatk_spark.config @@ -14,5 +14,3 @@ params { use_gatk_spark = 'baserecalibrator,markduplicates' input = "${projectDir}/tests/csv/3.0/fastq_tumor_only.csv" } - -docker.runOptions = '' diff --git a/modules/nf-core/gatk4spark/applybqsr/main.nf b/modules/nf-core/gatk4spark/applybqsr/main.nf index 170dbeeafd..70bd8b27c5 100644 --- a/modules/nf-core/gatk4spark/applybqsr/main.nf +++ b/modules/nf-core/gatk4spark/applybqsr/main.nf @@ -7,6 +7,10 @@ process GATK4SPARK_APPLYBQSR { 'https://depot.galaxyproject.org/singularity/gatk4-spark:4.4.0.0--hdfd78af_0': 'biocontainers/gatk4-spark:4.4.0.0--hdfd78af_0' }" + if (workflow.containerEngine == 'docker') { + containerOptions = '-u $(id -u):$(id -g) -v /etc/passwd:/etc/passwd:ro' + } + input: tuple val(meta), path(input), path(input_index), path(bqsr_table), path(intervals) path fasta diff --git a/modules/nf-core/gatk4spark/baserecalibrator/main.nf b/modules/nf-core/gatk4spark/baserecalibrator/main.nf index ee44bf7d66..3e4c4b3773 100644 --- a/modules/nf-core/gatk4spark/baserecalibrator/main.nf +++ b/modules/nf-core/gatk4spark/baserecalibrator/main.nf @@ -7,6 +7,10 @@ process GATK4SPARK_BASERECALIBRATOR { 'https://depot.galaxyproject.org/singularity/gatk4-spark:4.4.0.0--hdfd78af_0': 'biocontainers/gatk4-spark:4.4.0.0--hdfd78af_0' }" + if (workflow.containerEngine == 'docker') { + containerOptions = '-u $(id -u):$(id -g) -v /etc/passwd:/etc/passwd:ro' + } + input: tuple val(meta), path(input), path(input_index), path(intervals) path fasta diff --git a/modules/nf-core/gatk4spark/markduplicates/main.nf b/modules/nf-core/gatk4spark/markduplicates/main.nf index 61e295c839..2489c1fd6c 100644 --- a/modules/nf-core/gatk4spark/markduplicates/main.nf +++ b/modules/nf-core/gatk4spark/markduplicates/main.nf @@ -7,6 +7,10 @@ process GATK4SPARK_MARKDUPLICATES { 'https://depot.galaxyproject.org/singularity/gatk4-spark:4.4.0.0--hdfd78af_0': 'biocontainers/gatk4-spark:4.4.0.0--hdfd78af_0' }" + if (workflow.containerEngine == 'docker') { + containerOptions = '-u $(id -u):$(id -g) -v /etc/passwd:/etc/passwd:ro' + } + input: tuple val(meta), path(bam) path fasta diff --git a/nextflow.config b/nextflow.config index 25ab62c66f..c0eb9c702c 100644 --- a/nextflow.config +++ b/nextflow.config @@ -192,7 +192,7 @@ profiles { docker.enabled = true podman.enabled = false shifter.enabled = false - docker.runOptions = { params.use_gatk_spark ? '' : '-u $(id -u):$(id -g)' }.call() + docker.runOptions = '-u $(id -u):$(id -g)' singularity.enabled = false } arm { From ea92fd70d4d300653a7296d8260fe11ab7beeed7 Mon Sep 17 00:00:00 2001 From: asp8200 Date: Mon, 4 Mar 2024 22:09:19 +0000 Subject: [PATCH 2/2] Trigger CI-test of joint-germline --- tests/test_joint_germline.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/tests/test_joint_germline.yml b/tests/test_joint_germline.yml index 7b634193c6..4d61124784 100644 --- a/tests/test_joint_germline.yml +++ b/tests/test_joint_germline.yml @@ -4,6 +4,7 @@ - germline - joint_germline - variant_calling + - foo files: - path: results/csv/variantcalled.csv md5sum: d2dffdbd2b4f1f26a06637592d24dab3