Fix integration tests

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>

Author: pditommaso

.github/workflows/build.yml

@@ -143,7 +143,7 @@ jobs:
       - name: Run tests
         run: |
           cat $HOME/.nextflow/scm
-          make assemble install
+          make clean assemble install
           bash test-ci.sh
         env:
           TEST_JDK: ${{ matrix.java_version }}

packing.gradle

@@ -90,7 +90,7 @@ protected coordinates( it ) {
 /*
  * Compile and pack all packages
  */
-task packOne( dependsOn: [clean, compile, ":nextflow:shadowJar"]) {
+task packOne( dependsOn: [compile, ":nextflow:shadowJar"]) {
     doLast {
         def source = "modules/nextflow/build/libs/nextflow-${version}-one.jar"
         ant.copy(file: source, todir: releaseDir, overwrite: true)
@@ -99,7 +99,7 @@ task packOne( dependsOn: [clean, compile, ":nextflow:shadowJar"]) {
     }
 }
 
-task packDist( dependsOn: [clean, compile, ":nextflow:shadowJar"]) {
+task packDist( dependsOn: [compile, ":nextflow:shadowJar"]) {
 
     doLast {
         file(releaseDir).mkdirs()

test-ci.sh

@@ -16,7 +16,6 @@ fi
 export WITH_DOCKER='-with-docker'
 export NXF_PLUGINS_DIR=$PWD/build/plugins
 export NXF_CMD=$PWD/nextflow;
-export CAPSULE_LOG=none
 export TEST_JDK
 export TEST_MODE
 

validation/test.sh

@@ -46,14 +46,6 @@ if [[ $TEST_MODE == 'test_integration' ]]; then
     $NXF_CMD run nextflow-io/rnaseq-nf -with-docker $OPTS
     $NXF_CMD run nextflow-io/rnaseq-nf -with-docker $OPTS -resume
 
-    #
-    # RNASEQ-NF with async finalizer
-    #
-    echo nextflow-io/rnaseq-nf async finalizer
-    [[ $TOWER_ACCESS_TOKEN ]] && OPTS='-with-tower' || OPTS=''
-    NXF_ENABLE_ASYNC_FINALIZER=true $NXF_CMD run nextflow-io/rnaseq-nf -with-docker
-    NXF_ENABLE_ASYNC_FINALIZER=true $NXF_CMD run nextflow-io/rnaseq-nf -with-docker -resume
-
     exit 0
 fi