Merge pull request #1431 from asp8200/fix_docker_runoptions_II

Using process.containerOptions instead of docker.runOptions
nf-core · Mar 8, 2024 · 2e06e65 · 2e06e65
2 parents 355c354 + 1c35f21
commit 2e06e65
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Showing 8 changed files with 19 additions and 13 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -28,6 +28,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#1419](https://github.com/nf-core/sarek/pull/1419) - Updating GATK to v4.5, and updating samtools to v1.19.2 in GATK/markduplicates.
 - [#1426](https://github.com/nf-core/sarek/pull/1426) - Updating certain modules in order to fix the testdata-path in the nf-tests of those modules. Setting Docker runOptions for params.use_gatk_spark.
 - [#1428](https://github.com/nf-core/sarek/pull/1428) - Sync `TEMPLATE` with `tools` `2.13.1`
+- [#1431](https://github.com/nf-core/sarek/pull/1431) - Using docker.containerOptions instead of docker.runOptions. Clearing containerOptions for SPARK modules for any kind of supported container engine.
 
 ### Fixed
 

diff --git a/conf/modules/markduplicates.config b/conf/modules/markduplicates.config
@@ -91,6 +91,7 @@ process {
     }
 
     withName: 'GATK4SPARK_MARKDUPLICATES' {
+        containerOptions = ''
         ext.args   = { '--remove-sequencing-duplicates false -VS LENIENT' }
         ext.prefix = { "${meta.id}.md.cram" }
         publishDir = [

diff --git a/conf/modules/prepare_recalibration.config b/conf/modules/prepare_recalibration.config
@@ -16,6 +16,9 @@
 process {
 
     withName: 'GATK4_BASERECALIBRATOR|GATK4SPARK_BASERECALIBRATOR' {
+        if (params.use_gatk_spark) {
+            containerOptions = ''
+        }
         ext.prefix       = { meta.num_intervals <= 1 ? "${meta.id}.recal" : "${meta.id}_${intervals.simpleName}.recal" }
         publishDir       = [
             mode: params.publish_dir_mode,

diff --git a/conf/modules/recalibrate.config b/conf/modules/recalibrate.config
@@ -16,6 +16,9 @@
 process {
 
     withName: 'GATK4_APPLYBQSR|GATK4SPARK_APPLYBQSR' {
+        if (params.use_gatk_spark) {
+            containerOptions = ''
+        }
         ext.prefix       = { meta.num_intervals <= 1 ? "${meta.id}.recal" : "${meta.id}_${intervals.baseName}.recal" }
         publishDir       = [
             mode: params.publish_dir_mode,

diff --git 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()
+        process.containerOptions                 = '-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
@@ -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()
+        process.containerOptions                 = '-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
@@ -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/nextflow.config b/nextflow.config
@@ -186,17 +186,17 @@ profiles {
         singularity.enabled    = false
     }
     docker {
-        apptainer.enabled      = false
-        charliecloud.enabled   = false
-        conda.enabled          = false
-        docker.enabled         = true
-        podman.enabled         = false
-        shifter.enabled        = false
-        docker.runOptions      = { params.use_gatk_spark ? '' : '-u $(id -u):$(id -g)' }.call()
-        singularity.enabled    = false
+        apptainer.enabled        = false
+        charliecloud.enabled     = false
+        conda.enabled            = false
+        docker.enabled           = true
+        podman.enabled           = false
+        shifter.enabled          = false
+        process.containerOptions = '-u $(id -u):$(id -g)'
+        singularity.enabled      = false
     }
     arm {
-        docker.runOptions      = '-u $(id -u):$(id -g) --platform=linux/amd64'
+        process.containerOptions = '-u $(id -u):$(id -g) --platform=linux/amd64'
     }
     singularity {
         apptainer.enabled      = false