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Use AWS login in GitHub workflow - switch to Public ECR except for ba…
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emi80 committed Jun 19, 2024
1 parent 5d1d61d commit ab03909
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Showing 3 changed files with 38 additions and 5 deletions.
37 changes: 36 additions & 1 deletion .github/workflows/test.yml
Original file line number Diff line number Diff line change
Expand Up @@ -12,7 +12,12 @@ on:
env:
JAVA_VERSION: 17
JAVA_DISTRO: zulu

AWS_REGION: us-east-1

permissions:
id-token: write
contents: read

jobs:
pipeline-test:
name: Pipeline tests
Expand All @@ -32,6 +37,16 @@ jobs:

steps:
- uses: actions/checkout@v4
- name: Configure AWS credentials
uses: aws-actions/configure-aws-credentials@v4
with:
role-to-assume: arn:aws:iam::566365074765:role/github-actions-role
aws-region: ${{ env.AWS_REGION }}
- name: Login to Amazon ECR Public
id: login-ecr-public
uses: aws-actions/amazon-ecr-login@v2
with:
registry-type: public
- name: Set up Java
uses: actions/setup-java@v4
with:
Expand All @@ -53,6 +68,16 @@ jobs:

steps:
- uses: actions/checkout@v4
- name: Configure AWS credentials
uses: aws-actions/configure-aws-credentials@v4
with:
role-to-assume: arn:aws:iam::566365074765:role/github-actions-role
aws-region: ${{ env.AWS_REGION }}
- name: Login to Amazon ECR Public
id: login-ecr-public
uses: aws-actions/amazon-ecr-login@v2
with:
registry-type: public
- name: Set up Java
uses: actions/setup-java@v4
with:
Expand All @@ -72,6 +97,16 @@ jobs:

steps:
- uses: actions/checkout@v4
- name: Configure AWS credentials
uses: aws-actions/configure-aws-credentials@v4
with:
role-to-assume: arn:aws:iam::566365074765:role/github-actions-role
aws-region: ${{ env.AWS_REGION }}
- name: Login to Amazon ECR Public
id: login-ecr-public
uses: aws-actions/amazon-ecr-login@v2
with:
registry-type: public
- name: Set up Java
uses: actions/setup-java@v4
with:
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2 changes: 1 addition & 1 deletion modules/inferExp/rseqc/main.nf
Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,7 @@ params.rseqcVersion = '2.6.4--py27hf8a1672_2'
params.ucscVersion = '447--h2a80c09_1'
params.gtfToGenePredContainer = "${params.containerRepo}/ucsc-gtftogenepred:${params.ucscVersion}"
params.genePredContainer = "${params.containerRepo}/ucsc-genepredtobed:${params.ucscVersion}"
params.rseqcContainer = "public.ecr.aws/biocontainers/rseqc:${params.rseqcVersion}"
params.rseqcContainer = "${params.containerRepo}/rseqc:${params.rseqcVersion}"
params.inferExpThreshold = '0.8'

process gtfToGenePred {
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4 changes: 1 addition & 3 deletions nextflow.config
Original file line number Diff line number Diff line change
Expand Up @@ -11,7 +11,7 @@ params {
annotation = "$baseDir/data/annotation.gtf"
}

params.containerRepo = "quay.io/biocontainers"
params.containerRepo = "public.ecr.aws/biocontainers"

// Docker is disabled by default and uses the following options when activated
docker {
Expand Down Expand Up @@ -189,8 +189,6 @@ profiles {
params.contigTool = "RGCRG"
params.quantificationTool = "RSEM"

params.containerRepo = 'public.ecr.aws/biocontainers'

params.starVersion = '2.5.3a--0'
params.rsemVersion = '1.3.0--pl526r341h4f16992_4'
params.samtoolsVersion = '1.6--hc3601fc_10'
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