Getting rid of the dummy variable params.docker_enabled. Clearing con…

…tainerOptions for SPARK-modules for any kind of container engine.
asp8200 · Mar 8, 2024 · 3386da7 · 3386da7
1 parent 77cbebb
commit 3386da7
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Showing 6 changed files with 3 additions and 8 deletions.
diff --git a/conf/modules/markduplicates.config b/conf/modules/markduplicates.config
@@ -91,9 +91,7 @@ process {
     }
 
     withName: 'GATK4SPARK_MARKDUPLICATES' {
-        if (params.use_gatk_spark && params.docker_enabled) {
-            containerOptions = ''
-        }
+        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
@@ -16,7 +16,7 @@
 process {
 
     withName: 'GATK4_BASERECALIBRATOR|GATK4SPARK_BASERECALIBRATOR' {
-        if (params.use_gatk_spark && params.docker_enabled) {
+        if (params.use_gatk_spark) {
             containerOptions = ''
         }
         ext.prefix       = { meta.num_intervals <= 1 ? "${meta.id}.recal" : "${meta.id}_${intervals.simpleName}.recal" }

diff --git a/conf/modules/recalibrate.config b/conf/modules/recalibrate.config
@@ -16,7 +16,7 @@
 process {
 
     withName: 'GATK4_APPLYBQSR|GATK4SPARK_APPLYBQSR' {
-        if (params.use_gatk_spark && params.docker_enabled) {
+        if (params.use_gatk_spark) {
             containerOptions = ''
         }
         ext.prefix       = { meta.num_intervals <= 1 ? "${meta.id}.recal" : "${meta.id}_${intervals.baseName}.recal" }

diff --git a/conf/test.config b/conf/test.config
@@ -108,7 +108,6 @@ if (System.getenv('PROFILE')) {
     } else if ("$PROFILE" == "docker") {
         conda.enabled                            = false
         docker.enabled                           = true
-        params.docker_enabled                    = true
         process.containerOptions                 = '-u $(id -u):$(id -g)'
         charliecloud.enabled                     = false
         podman.enabled                           = false

diff --git a/conf/test/cache.config b/conf/test/cache.config
@@ -116,7 +116,6 @@ if (System.getenv('PROFILE')) {
     } else if ("$PROFILE" == "docker") {
         conda.enabled                            = false
         docker.enabled                           = true
-        params.docker_enabled                    = true
         process.containerOptions                 = '-u $(id -u):$(id -g)'
         charliecloud.enabled                     = false
         podman.enabled                           = false

diff --git a/nextflow.config b/nextflow.config
@@ -7,7 +7,6 @@
 */
 
 params {
-    docker_enabled  = false
     // Workflow flags:
 
     // Mandatory arguments