fix(test): set config yaml only if preset is disabled

.github/workflows/workflow_modules.yml

@@ -442,14 +442,15 @@ jobs:
           OUTPUT=outputEasy
           bash ./scripts/test_settings.sh \
           " --preset --scratch /vol/scratch --input.paired.path test_data/fullPipeline/reads_split.tsv --highmemLarge=28,2000 --s3SignIn false  --databases=/vol/scratch/databases/ --output=${OUTPUT} " \
-          "" "${WORK_DIR}" ${PROFILE} ${VERSION} || exit 1
+          "   " "${WORK_DIR}" ${PROFILE} ${VERSION} "preset" || exit 1
+          bash ./scripts/check_parameter.sh ${OUTPUT} || exit 1
       - name: Test whether settings in default mode can be updated
         run: |
           VERSION=$(sort VERSIONS.txt | tail -n 1)
           OUTPUT=outputDefault
           bash ./scripts/test_settings.sh \
           "  --scratch /vol/scratch  --resources.highmemLarge.memory=2000 --s3SignIn false  --databases=/vol/scratch/databases/ --output=${OUTPUT}  " \
-          "" "${WORK_DIR}" ${PROFILE} ${VERSION} || exit 1
+          " -params-file /example_params/fullPipeline.yml " "${WORK_DIR}" ${PROFILE} ${VERSION} "" || exit 1
           bash ./scripts/check_parameter.sh ${OUTPUT} || exit 1
 
 

Makefile

@@ -29,6 +29,15 @@ ifndef PARAMS_FILE
 	override PARAMS_FILE = ${CURRENT_DIR}/example_params/fullPipeline.yml
 endif
 
+ifdef PRESET
+	override PARAMS_FILE=""
+endif
+
+ifneq (${PARAMS_FILE}, "")
+	override PARAMS_COMMAND =  -params-file ${PARAMS_FILE}
+endif
+
+
 ifndef BRANCH
 	override BRANCH = "dev"
 endif
@@ -126,7 +135,7 @@ set_secrets: nextflow ## Set secrets for sensitive data access
 	NXF_HOME=$$PWD/.nextflow ./nextflow secrets set ${SECRET_NAME} ${SECRET_VALUE}
 
 run_small_full_test: nextflow ## Prepares input files like downloading bins and reads and executes Nextflow. The default configuration it runs the full pipeline locally.
-	NXF_HOME=$$PWD/.nextflow ./nextflow run main.nf ${OPTIONS} -work-dir ${WORK_DIR} -profile ${PROFILE} -resume -entry ${ENTRY} -params-file ${PARAMS_FILE} --logDir ${LOG_DIR} ; exit $$?
+	NXF_HOME=$$PWD/.nextflow ./nextflow run main.nf ${OPTIONS} -work-dir ${WORK_DIR} -profile ${PROFILE} -resume -entry ${ENTRY} ${PARAMS_COMMAND} --logDir ${LOG_DIR} ; exit $$?
 
 
 help: ## Lists available Makefile commands

nextflow.config

@@ -180,7 +180,7 @@ def getPresetInput(){
 *
 */
 def getPresetResources(){
-   resources = preLoadYML["resources"]
+   def resources = preLoadYML["resources"]
    System.out.println(PRETTY_SEPARATOR)
    System.out.println("The following job flavors are defined:\n")
 
@@ -192,15 +192,13 @@ def getPresetResources(){
      ram = resources[flavorSize]["memory"]
 
      if(params.containsKey(flavorSize)){
-
        cpus = params[flavorSize].split(",")[CPUS_KEY] as Integer
        ram = params[flavorSize].split(",")[MEMORY_KEY] as Integer
        resources[flavorSize]["cpus"] = cpus
        resources[flavorSize]["memory"] = ram
      }
      System.out.println("Flavor:" + flavorSize + ", CPUs:" + cpus + ", Memory:" + ram)
    }
-
    return resources
 }
 

scripts/test_settings.sh

@@ -2,16 +2,19 @@ set -e
 
 ENTRY="wSaveSettings"
 OPTIONS=$1
-YAML="${2:-example_params/fullPipeline.yml}"
+YAML="$2"
 WORK="${3:-work}_${ENTRY}"
 PROFILE="${4:-standard}"
 VERSION="${5:-}"
+PRESET="${6:-}"
 LOG_DIR="${WORK}/logs"
 make run_small_full_test WORK_DIR=${WORK} \
-	        PARAMS_FILE=$YAML \
+	        PARAMS_FILE="$YAML" \
+		PRESET="${PRESET}" \
 		LOG_DIR=${LOG_DIR} \
 		PROFILE="$PROFILE" \
 	        OPTIONS=" $OPTIONS " \
 	        ENTRY="${ENTRY}" \
 	        VERSION="$VERSION" 
 
+make check LOG_DIR=${LOG_DIR}