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Enable wave gcp test #5490

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merged 4 commits into from
Nov 10, 2024
Merged

Enable wave gcp test #5490

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f4549da
Enable wave gcp test
tom-seqera Nov 8, 2024
679815d
Fix google env + tests
pditommaso Nov 10, 2024
6f17c29
Fix tests
pditommaso Nov 10, 2024
0cde0c8
Revert test modes [ci skip]
pditommaso Nov 10, 2024
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6 changes: 6 additions & 0 deletions .github/workflows/build.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -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 > $PWD/google_credentials.json
Expand Down Expand Up @@ -158,6 +159,11 @@ jobs:
- name: Run tests
run: |
env | sort
# configure test env
if [[ "$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
Expand Down
3 changes: 0 additions & 3 deletions validation/google.sh
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Expand Up @@ -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

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11 changes: 0 additions & 11 deletions validation/wave-tests/example6/nextflow.config
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@@ -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'
Expand All @@ -16,5 +7,3 @@ fusion {
enabled = true
}

workDir = 's3://nextflow-ci/wave'

2 changes: 1 addition & 1 deletion validation/wave-tests/example6/run-aws.sh
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@@ -1,6 +1,6 @@
$NXF_CMD run \
rnaseq-nf \
-profile batch \
-profile batch,s3-data \
-with-wave \
-with-fusion \
-process.scratch false
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2 changes: 1 addition & 1 deletion validation/wave-tests/example6/run-gcp.sh
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
$NXF_CMD run \
rnaseq-nf \
-profile gcb \
-profile google-batch,gs-data \
-with-wave \
-with-fusion \
-process.scratch false
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5 changes: 4 additions & 1 deletion validation/wave-tests/example6/run.sh
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@@ -1,2 +1,5 @@
$NXF_CMD run rnaseq-nf -with-wave
$NXF_CMD run \
rnaseq-nf \
-with-wave \
-w s3://nextflow-ci/wave

2 changes: 1 addition & 1 deletion validation/wave.sh
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Expand Up @@ -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)