diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml index 3cf322c98de..9a8675a0135 100644 --- 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 $HOME/.nextflow/scm make clean assemble install bash test-ci.sh diff --git a/validation/google.sh b/validation/google.sh index 8dcda8ab99f..0dcb9606f8c 100644 --- a/validation/google.sh +++ b/validation/google.sh @@ -6,9 +6,6 @@ get_abs_filename() { export NXF_CMD=${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 index f58834306ff..c757b3bb7b4 100644 --- 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 index b63724d33c4..0f2d2247fa9 100644 --- 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 index b522ac13c51..c55dcdb3ecc 100644 --- a/validation/wave-tests/example6/run-gcp.sh +++ b/validation/wave-tests/example6/run-gcp.sh @@ -1,6 +1,6 @@ $NXF_CMD run \ rnaseq-nf \ - -profile gcb \ + -profile google-batch,gs-data \ -with-wave \ -with-fusion \ -process.scratch false diff --git a/validation/wave-tests/example6/run.sh b/validation/wave-tests/example6/run.sh index 0bb6d254c5b..971a65f3517 100644 --- a/validation/wave-tests/example6/run.sh +++ b/validation/wave-tests/example6/run.sh @@ -1,2 +1,5 @@ -$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 index 6b8953a7f30..b24b718be6a 100644 --- 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)