From 7761b03e2a47e79aee17bab730462006e3903cab Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Wed, 21 Oct 2020 09:23:16 +0200 Subject: [PATCH 1/5] Try patching AWS fulltest command --- .github/workflows/awsfulltest.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml index 0561d87ac..db0984549 100644 --- a/.github/workflows/awsfulltest.yml +++ b/.github/workflows/awsfulltest.yml @@ -36,4 +36,4 @@ jobs: --job-name nf-core-eager \ --job-queue $AWS_JOB_QUEUE \ --job-definition $AWS_JOB_DEFINITION \ - --container-overrides '{"command": ["nf-core/eager", "-r '"${GITHUB_SHA}"' -profile awsfulltest --outdir s3://'"${AWS_S3_BUCKET}"'/eager/results-'"${GITHUB_SHA}"' -w s3://'"${AWS_S3_BUCKET}"'/eager/work-'"${GITHUB_SHA}"' -with-tower"], "environment": [{"name": "TOWER_ACCESS_TOKEN", "value": "'"$TOWER_ACCESS_TOKEN"'"}]}' + --container-overrides '{"command": ["nf-core/eager", "-r '"${GITHUB_SHA}"' -profile awsfulltest --outdir s3://'"${AWS_S3_BUCKET}"'/eager/results-'"${GITHUB_SHA}"' -w s3://'"${AWS_S3_BUCKET}"'/eager/work-'"${GITHUB_SHA}"' -with-tower"], "environment": [{"name": "TOWER_ACCESS_TOKEN", "value": '"$TOWER_ACCESS_TOKEN"'}]}' From e28fcb333c8fc24ec609d137680a821ca2e16eb3 Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Wed, 21 Oct 2020 09:32:41 +0200 Subject: [PATCH 2/5] Also update aws test --- .github/workflows/awstest.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/awstest.yml b/.github/workflows/awstest.yml index f1fc1621f..4f334965a 100644 --- a/.github/workflows/awstest.yml +++ b/.github/workflows/awstest.yml @@ -36,4 +36,4 @@ jobs: --job-name nf-core-eager \ --job-queue $AWS_JOB_QUEUE \ --job-definition $AWS_JOB_DEFINITION \ - --container-overrides '{"command": ["nf-core/eager", "-r '"${GITHUB_SHA}"' -profile test_tsv_complex --outdir s3://'"${AWS_S3_BUCKET}"'/eager/results-'"${GITHUB_SHA}"' -w s3://'"${AWS_S3_BUCKET}"'/eager/work-'"${GITHUB_SHA}"' -with-tower"], "environment": [{"name": "TOWER_ACCESS_TOKEN", "value": "'"$TOWER_ACCESS_TOKEN"'"}]}'eager/work-'"${GITHUB_SHA}"' -with-tower"], "environment": [{"name": "TOWER_ACCESS_TOKEN", "value": "'"$TOWER_ACCESS_TOKEN"'"}]}' + --container-overrides '{"command": ["nf-core/eager", "-r '"${GITHUB_SHA}"' -profile test_tsv_complex --outdir s3://'"${AWS_S3_BUCKET}"'/eager/results-'"${GITHUB_SHA}"' -w s3://'"${AWS_S3_BUCKET}"'/eager/work-'"${GITHUB_SHA}"' -with-tower"], "environment": [{"name": "TOWER_ACCESS_TOKEN", "value": "'"$TOWER_ACCESS_TOKEN"'"}]}'eager/work-'"${GITHUB_SHA}"' -with-tower"], "environment": [{"name": "TOWER_ACCESS_TOKEN", "value": '"$TOWER_ACCESS_TOKEN"'}]}' From dcd8bad698fea81294bf6314134c851c614b25b7 Mon Sep 17 00:00:00 2001 From: James Fellows Yates Date: Wed, 21 Oct 2020 09:55:44 +0200 Subject: [PATCH 3/5] Use dev version of AWS templates --- .github/workflows/awsfulltest.yml | 8 +++++--- .github/workflows/awstest.yml | 6 ++++-- 2 files changed, 9 insertions(+), 5 deletions(-) diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml index db0984549..0ad28af59 100644 --- a/.github/workflows/awsfulltest.yml +++ b/.github/workflows/awsfulltest.yml @@ -1,10 +1,12 @@ - name: nf-core AWS full size tests -# This workflow is triggered on push to the master branch. +# This workflow is triggered on published releases. +# It can be additionally triggered manually with GitHub actions workflow dispatch. +# It runs the -profile 'test_full' on AWS batch on: release: types: [published] + workflow_dispatch: jobs: run-awstest: @@ -36,4 +38,4 @@ jobs: --job-name nf-core-eager \ --job-queue $AWS_JOB_QUEUE \ --job-definition $AWS_JOB_DEFINITION \ - --container-overrides '{"command": ["nf-core/eager", "-r '"${GITHUB_SHA}"' -profile awsfulltest --outdir s3://'"${AWS_S3_BUCKET}"'/eager/results-'"${GITHUB_SHA}"' -w s3://'"${AWS_S3_BUCKET}"'/eager/work-'"${GITHUB_SHA}"' -with-tower"], "environment": [{"name": "TOWER_ACCESS_TOKEN", "value": '"$TOWER_ACCESS_TOKEN"'}]}' + --container-overrides '{"command": ["nf-core/eager", "-r '"${GITHUB_SHA}"' -profile test --outdir s3://'"${AWS_S3_BUCKET}"'/eager/results-'"${GITHUB_SHA}"' -w s3://'"${AWS_S3_BUCKET}"'/eager/work-'"${GITHUB_SHA}"' -with-tower"], "environment": [{"name": "TOWER_ACCESS_TOKEN", "value": "'"$TOWER_ACCESS_TOKEN"'"}]}' diff --git a/.github/workflows/awstest.yml b/.github/workflows/awstest.yml index 4f334965a..0877df3c6 100644 --- a/.github/workflows/awstest.yml +++ b/.github/workflows/awstest.yml @@ -1,11 +1,13 @@ name: nf-core AWS test # This workflow is triggered on push to the master branch. -# It runs the -profile 'test' on AWS batch +# It can be additionally triggered manually with GitHub actions workflow dispatch. +# It runs the -profile 'test' on AWS batch. on: push: branches: - master + workflow_dispatch: jobs: run-awstest: @@ -36,4 +38,4 @@ jobs: --job-name nf-core-eager \ --job-queue $AWS_JOB_QUEUE \ --job-definition $AWS_JOB_DEFINITION \ - --container-overrides '{"command": ["nf-core/eager", "-r '"${GITHUB_SHA}"' -profile test_tsv_complex --outdir s3://'"${AWS_S3_BUCKET}"'/eager/results-'"${GITHUB_SHA}"' -w s3://'"${AWS_S3_BUCKET}"'/eager/work-'"${GITHUB_SHA}"' -with-tower"], "environment": [{"name": "TOWER_ACCESS_TOKEN", "value": "'"$TOWER_ACCESS_TOKEN"'"}]}'eager/work-'"${GITHUB_SHA}"' -with-tower"], "environment": [{"name": "TOWER_ACCESS_TOKEN", "value": '"$TOWER_ACCESS_TOKEN"'}]}' + --container-overrides '{"command": ["nf-core/eager", "-r '"${GITHUB_SHA}"' -profile test --outdir s3://'"${AWS_S3_BUCKET}"'/eager/results-'"${GITHUB_SHA}"' -w s3://'"${AWS_S3_BUCKET}"'/eager/work-'"${GITHUB_SHA}"' -with-tower"], "environment": [{"name": "TOWER_ACCESS_TOKEN", "value": "'"$TOWER_ACCESS_TOKEN"'"}]}' \ No newline at end of file From b2e5719a6cf394beee5dbd12c3a6e76ebce01780 Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Wed, 21 Oct 2020 09:58:04 +0200 Subject: [PATCH 4/5] Update awsfulltest.yml --- .github/workflows/awsfulltest.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml index 0ad28af59..5a6da0eca 100644 --- a/.github/workflows/awsfulltest.yml +++ b/.github/workflows/awsfulltest.yml @@ -38,4 +38,4 @@ jobs: --job-name nf-core-eager \ --job-queue $AWS_JOB_QUEUE \ --job-definition $AWS_JOB_DEFINITION \ - --container-overrides '{"command": ["nf-core/eager", "-r '"${GITHUB_SHA}"' -profile test --outdir s3://'"${AWS_S3_BUCKET}"'/eager/results-'"${GITHUB_SHA}"' -w s3://'"${AWS_S3_BUCKET}"'/eager/work-'"${GITHUB_SHA}"' -with-tower"], "environment": [{"name": "TOWER_ACCESS_TOKEN", "value": "'"$TOWER_ACCESS_TOKEN"'"}]}' + --container-overrides '{"command": ["nf-core/eager", "-r '"${GITHUB_SHA}"' -profile awsfulltest --outdir s3://'"${AWS_S3_BUCKET}"'/eager/results-'"${GITHUB_SHA}"' -w s3://'"${AWS_S3_BUCKET}"'/eager/work-'"${GITHUB_SHA}"' -with-tower"], "environment": [{"name": "TOWER_ACCESS_TOKEN", "value": "'"$TOWER_ACCESS_TOKEN"'"}]}' From 0b5e90b2191b83baee916fda6a969bc3acbf9d35 Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Wed, 21 Oct 2020 09:58:21 +0200 Subject: [PATCH 5/5] Update awstest.yml --- .github/workflows/awstest.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/awstest.yml b/.github/workflows/awstest.yml index 0877df3c6..4686416a8 100644 --- a/.github/workflows/awstest.yml +++ b/.github/workflows/awstest.yml @@ -38,4 +38,4 @@ jobs: --job-name nf-core-eager \ --job-queue $AWS_JOB_QUEUE \ --job-definition $AWS_JOB_DEFINITION \ - --container-overrides '{"command": ["nf-core/eager", "-r '"${GITHUB_SHA}"' -profile test --outdir s3://'"${AWS_S3_BUCKET}"'/eager/results-'"${GITHUB_SHA}"' -w s3://'"${AWS_S3_BUCKET}"'/eager/work-'"${GITHUB_SHA}"' -with-tower"], "environment": [{"name": "TOWER_ACCESS_TOKEN", "value": "'"$TOWER_ACCESS_TOKEN"'"}]}' \ No newline at end of file + --container-overrides '{"command": ["nf-core/eager", "-r '"${GITHUB_SHA}"' -profile test_tsv_complex --outdir s3://'"${AWS_S3_BUCKET}"'/eager/results-'"${GITHUB_SHA}"' -w s3://'"${AWS_S3_BUCKET}"'/eager/work-'"${GITHUB_SHA}"' -with-tower"], "environment": [{"name": "TOWER_ACCESS_TOKEN", "value": "'"$TOWER_ACCESS_TOKEN"'"}]}'