Fix wave GCP test (nextflow-io#5490)

Signed-off-by: Tom Sellman <tom.sellman@seqera.io> Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com> Co-authored-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
alberto-miranda · Nov 19, 2024 · 86f7712 · 86f7712
1 parent d253adf
commit 86f7712
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Showing 7 changed files with 13 additions and 18 deletions.
diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
@@ -90,6 +90,7 @@ jobs:
       - name: Test
         if: steps.changed-files.outputs.any_changed == 'true'
         run: |
+            env | sort
             # configure test env
             if [[ "$GOOGLE_SECRET" ]]; then
             echo $GOOGLE_SECRET | base64 -d > $PWD/google_credentials.json
@@ -158,6 +159,11 @@ jobs:
       - name: Run tests
         run: |
           env | sort
+          # configure test env
+          if [[ "$GOOGLE_SECRET" ]]; then
+          echo $GOOGLE_SECRET | base64 -d > $PWD/google_credentials.json
+          export GOOGLE_APPLICATION_CREDENTIALS=$PWD/google_credentials.json
+          fi
           cat $HOME/.nextflow/scm
           make clean assemble install
           bash test-ci.sh

diff --git a/validation/google.sh b/validation/google.sh
@@ -6,9 +6,6 @@ get_abs_filename() {
 
 export NXF_CMD=${NXF_CMD:-$(get_abs_filename ../launch.sh)}
 
-echo $GOOGLE_SECRET | base64 -d > $PWD/google_credentials.json
-export GOOGLE_APPLICATION_CREDENTIALS=$PWD/google_credentials.json
-
 [[ $TOWER_ACCESS_TOKEN ]] && OPTS='-with-tower' || OPTS=''
 set -x
 

diff --git a/validation/wave-tests/example6/nextflow.config b/validation/wave-tests/example6/nextflow.config
@@ -1,12 +1,3 @@
-process {
-  container = 'quay.io/nextflow/rnaseq-nf:v1.1'
-}
-
-params {
-  reads = 's3://rnaseq-nf/data/ggal/lung_{1,2}.fq'
-  transcriptome = 's3://rnaseq-nf/data/ggal/transcript.fa'
-}
-
 docker {
   enabled = true
   envWhitelist = 'AWS_ACCESS_KEY_ID,AWS_SECRET_ACCESS_KEY'
@@ -16,5 +7,3 @@ fusion {
   enabled = true
 }
 
-workDir = 's3://nextflow-ci/wave'
-
diff --git a/validation/wave-tests/example6/run-aws.sh b/validation/wave-tests/example6/run-aws.sh
@@ -1,6 +1,6 @@
 $NXF_CMD run \
     rnaseq-nf \
-    -profile batch \
+    -profile batch,s3-data \
     -with-wave \
     -with-fusion \
     -process.scratch false

diff --git a/validation/wave-tests/example6/run-gcp.sh b/validation/wave-tests/example6/run-gcp.sh
@@ -1,6 +1,6 @@
 $NXF_CMD run \
     rnaseq-nf \
-    -profile gcb \
+    -profile google-batch,gs-data \
     -with-wave \
     -with-fusion \
     -process.scratch false

diff --git a/validation/wave-tests/example6/run.sh b/validation/wave-tests/example6/run.sh
@@ -1,2 +1,5 @@
-$NXF_CMD run rnaseq-nf -with-wave
+$NXF_CMD run \
+    rnaseq-nf \
+    -with-wave \
+    -w s3://nextflow-ci/wave
 
diff --git a/validation/wave.sh b/validation/wave.sh
@@ -25,4 +25,4 @@ echo "Test Wave running rnaseq-nf with Fusion on AWS Batch"
 (cd wave-tests/example6; bash run-aws.sh)
 
 echo "Test Wave running rnaseq-nf with Fusion on Google Batch"
-(cd wave-tests/example6; bash run-aws.sh)
+(cd wave-tests/example6; bash run-gcp.sh)