From a8ed7e87b1c9291375f60cae67fef4ce1c2ad402 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Mon, 19 Jun 2023 10:29:03 +0200 Subject: [PATCH 1/2] remove public_aws_ecr --- .github/workflows/awsfulltest.yml | 2 +- .github/workflows/awsfulltest_germline.yml | 2 +- .github/workflows/awstest.yml | 2 +- conf/public_aws_ecr.config | 73 ---------------------- nextflow.config | 3 - 5 files changed, 3 insertions(+), 79 deletions(-) delete mode 100644 conf/public_aws_ecr.config diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml index 9a41b26a0e..401222be25 100644 --- a/.github/workflows/awsfulltest.yml +++ b/.github/workflows/awsfulltest.yml @@ -26,7 +26,7 @@ jobs: "hook_url": "${{ secrets.MEGATESTS_ALERTS_SLACK_HOOK_URL }}", "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/sarek/results-${{ github.sha }}/somatic_test" } - profiles: test_full,public_aws_ecr + profiles: test_full - uses: actions/upload-artifact@v3 with: name: Tower debug log file diff --git a/.github/workflows/awsfulltest_germline.yml b/.github/workflows/awsfulltest_germline.yml index 0e9867e4f2..bd9cf6c342 100644 --- a/.github/workflows/awsfulltest_germline.yml +++ b/.github/workflows/awsfulltest_germline.yml @@ -26,7 +26,7 @@ jobs: "hook_url": "${{ secrets.MEGATESTS_ALERTS_SLACK_HOOK_URL }}", "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/sarek/results-${{ github.sha }}/germline_test" } - profiles: test_full_germline,public_aws_ecr + profiles: test_full_germline - uses: actions/upload-artifact@v3 with: name: Tower debug log file diff --git a/.github/workflows/awstest.yml b/.github/workflows/awstest.yml index d1c521fd7f..ae40b9538f 100644 --- a/.github/workflows/awstest.yml +++ b/.github/workflows/awstest.yml @@ -22,7 +22,7 @@ jobs: { "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/sarek/results-test-${{ github.sha }}" } - profiles: test,public_aws_ecr + profiles: test - uses: actions/upload-artifact@v3 with: name: Tower debug log file diff --git a/conf/public_aws_ecr.config b/conf/public_aws_ecr.config deleted file mode 100644 index 75ff69f723..0000000000 --- a/conf/public_aws_ecr.config +++ /dev/null @@ -1,73 +0,0 @@ -/* -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - AWS ECR Config -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - Config to set public AWS ECR images wherever possible - This improves speed when running on AWS infrastructure. - Use this as an example template when using your own private registry. ----------------------------------------------------------------------------------------- -*/ - -docker.registry = 'public.ecr.aws' -podman.registry = 'public.ecr.aws' -singularity.registry = 'public.ecr.aws' - -process { - withName: 'ADD_INFO_TO_VCF' { - container = 'quay.io/biocontainers/gawk:5.1.0' - } - withName: 'ASCAT' { - container = 'quay.io/biocontainers/mulled-v2-c278c7398beb73294d78639a864352abef2931ce:ba3e6d2157eac2d38d22e62ec87675e12adb1010-0' - } - withName: 'BUILD_INTERVALS' { - container = 'quay.io/biocontainers/gawk:5.1.0' - } - withName: 'BWAMEM2_MEM' { - container = 'quay.io/biocontainers/mulled-v2-e5d375990341c5aef3c9aff74f96f66f65375ef6:2cdf6bf1e92acbeb9b2834b1c58754167173a410-0' - } - withName: 'BWA_MEM' { - container = 'quay.io/biocontainers/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:219b6c272b25e7e642ae3ff0bf0c5c81a5135ab4-0' - } - withName: 'CAT_CAT' { - container = 'quay.io/biocontainers/pigz:2.3.4' - } - withName: 'CAT_FASTQ' { - container = 'quay.io/nf-core/ubuntu:20.04' - } - withName: 'CNVKIT_BATCH' { - container = 'quay.io/biocontainers/mulled-v2-780d630a9bb6a0ff2e7b6f730906fd703e40e98f:3bdd798e4b9aed6d3e1aaa1596c913a3eeb865cb-0' - } - withName: 'CREATE_INTERVALS_BED' { - container = 'quay.io/biocontainers/gawk:5.1.0' - } - withName: 'DEEPVARIANT' { - container = 'quay.io/nf-core/deepvariant:1.5.0' - } - withName: 'DRAGMAP_ALIGN' { - container = 'quay.io/biocontainers/mulled-v2-580d344d9d4a496cd403932da8765f9e0187774d:5ebebbc128cd624282eaa37d2c7fe01505a91a69-0' - } - withName: 'GATK4_APPLYBQSR_SPARK' { - container = 'quay.io/nf-core/gatk:4.4.0.0' - } - withName: 'GATK4_BASERECALIBRATOR_SPARK' { - container = 'quay.io/nf-core/gatk:4.4.0.0' - } - withName: 'GATK4_CNNSCOREVARIANTS' { - container = 'quay.io/nf-core/gatk:4.4.0.0' - } - withName: 'GATK4_MARKDUPLICATES_SPARK' { - container = 'quay.io/nf-core/gatk:4.4.0.0' - } - withName: 'SAMBLASTER' { - container = 'quay.io/biocontainers/mulled-v2-19fa9f1a5c3966b63a24166365e81da35738c5ab:cee56b506ceb753d4bbef7e05b81e1bfc25d937f-0' - } - withName: 'SVDB_MERGE' { - container = 'quay.io/biocontainers/mulled-v2-c8daa8f9d69d3c5a1a4ff08283a166c18edb0000:af6f8534cd538a85ff43a2eae1b52b143e7abd05-0' - } - withName: 'UNTAR' { - container = 'quay.io/nf-core/ubuntu:20.04' - } - withName: 'UNZIP' { - container = 'quay.io/biocontainers/p7zip:16.02' - } -} diff --git a/nextflow.config b/nextflow.config index f94154dd0b..728c73c44a 100644 --- a/nextflow.config +++ b/nextflow.config @@ -234,9 +234,6 @@ profiles { executor.memory = 60.GB executor.name = 'local' } - public_aws_ecr { - includeConfig 'conf/public_aws_ecr.config' - } // Basic test profile for CI test { includeConfig 'conf/test.config' } test_cache { includeConfig 'conf/test/cache.config' } From db59f4974ddf9d38e1bab89c3c409bf5d9243f78 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Mon, 19 Jun 2023 12:06:23 +0200 Subject: [PATCH 2/2] update CHANGELOG --- CHANGELOG.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index c251401f6b..f4588b67be 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -15,6 +15,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### Fixed +- [#1118](https://github.com/nf-core/sarek/pull/1118) - Remove `public_aws_ecr` profile + ## [3.2.2](https://github.com/nf-core/sarek/releases/tag/3.2.2) - Vuoinesluobbalah Vuoinesluobbalah is a lake close to Bierikjávrre.