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Dummy PR : testing docker container options in GATK Spark modules #1430

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Mar 8, 2024
Merged

Dummy PR : testing docker container options in GATK Spark modules #1430

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de6ebf8
Using containerOptions for GATK Spark modules
asp8200 Mar 4, 2024
ea92fd7
Trigger CI-test of joint-germline
asp8200 Mar 4, 2024
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2 changes: 1 addition & 1 deletion conf/test.config
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Expand Up @@ -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
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2 changes: 1 addition & 1 deletion conf/test/cache.config
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Expand Up @@ -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
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2 changes: 0 additions & 2 deletions conf/test/use_gatk_spark.config
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Expand Up @@ -14,5 +14,3 @@ params {
use_gatk_spark = 'baserecalibrator,markduplicates'
input = "${projectDir}/tests/csv/3.0/fastq_tumor_only.csv"
}

docker.runOptions = ''
4 changes: 4 additions & 0 deletions modules/nf-core/gatk4spark/applybqsr/main.nf
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4 changes: 4 additions & 0 deletions modules/nf-core/gatk4spark/baserecalibrator/main.nf
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4 changes: 4 additions & 0 deletions modules/nf-core/gatk4spark/markduplicates/main.nf
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2 changes: 1 addition & 1 deletion nextflow.config
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Expand Up @@ -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 {
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1 change: 1 addition & 0 deletions tests/test_joint_germline.yml
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Expand Up @@ -4,6 +4,7 @@
- germline
- joint_germline
- variant_calling
- foo
files:
- path: results/csv/variantcalled.csv
md5sum: d2dffdbd2b4f1f26a06637592d24dab3
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