Adds public_aws_ecr profile for using ECR hosted images.

.github/workflows/awsfulltest.yml

@@ -25,7 +25,7 @@ jobs:
             {
               "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/sarek/results-${{ github.sha }}/somatic_test"
             }
-          profiles: test_full,aws_tower
+          profiles: test_full,public_aws_tower
       - uses: actions/upload-artifact@v3
         with:
           name: Tower debug log file

.github/workflows/awstest.yml

@@ -22,7 +22,7 @@ jobs:
             {
               "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/sarek/results-test-${{ github.sha }}"
             }
-          profiles: test,aws_tower
+          profiles: test,public_aws_tower
       - uses: actions/upload-artifact@v3
         with:
           name: Tower debug log file

CHANGELOG.md

@@ -19,6 +19,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#978](https://github.com/nf-core/sarek/pull/978) - Validate that patient/sample does not contain spaces
 - [#981](https://github.com/nf-core/sarek/pull/981) - Added documentation on generating ASCAT resources for exome and targeted sequencing
 - [#1041](https://github.com/nf-core/sarek/pull/1041) - Add params `vep_custom_args` to let user specify custom params more easily for `VEP`
+- [#1045](https://github.com/nf-core/sarek/pull/1045) - Add `public_aws_ecr` for using ECR hosted containers.
 
 ### Changed
 

conf/public_aws_ecr.config

@@ -0,0 +1,60 @@
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    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'
+
+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: 'DRAGMAP_ALIGN' {
+        container = 'quay.io/biocontainers/mulled-v2-580d344d9d4a496cd403932da8765f9e0187774d:5ebebbc128cd624282eaa37d2c7fe01505a91a69-0'
+    }
+    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'
+    }
+    withName: 'VCFTOOLS' {
+        container = 'public.ecr.aws/biocontainers/vcftools:0.1.16--pl5321hd03093a_7'
+    }
+}

nextflow.config

@@ -235,6 +235,9 @@ 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/test.config' }
     // Extra test profiles for full tests on AWS