Merge pull request #166 from adamrtalbot/public_aws_ecr_profile

Add public_aws_ecr profile for using public ECR images

.github/workflows/awsfulltest.yml

@@ -24,7 +24,7 @@ jobs:
             {
               "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/hic/results-${{ github.sha }}"
             }
-          profiles: test_full,aws_tower
+          profiles: test_full,public_aws_ecr
       - uses: actions/upload-artifact@v3
         with:
           name: Tower debug log file

.github/workflows/awstest.yml

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

.github/workflows/ci.yml

@@ -31,7 +31,7 @@ jobs:
         uses: actions/checkout@v3
 
       - name: Install Nextflow
-        uses: nf-core/setup-nextflow@v1
+        uses: nf-core/setup-nextflow@v1.3.0
         with:
           version: "${{ matrix.NXF_VER }}"
 

CHANGELOG.md

@@ -5,6 +5,12 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## v2.1.0dev
 
+### `Added`
+
+- Added public_aws_ecr profile for using containers stored on ECR.
+
+### `Fixed`
+
 ## v2.0.0 - 2023-01-12
 
 ### `Added`

conf/public_aws_ecr.config

+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    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: '.*:BOWTIE2_ALIGN' {
+        container = 'quay.io/biocontainers/mulled-v2-ac74a7f02cebcfcc07d8e8d1d750af9c83b4d45a:a0ffedb52808e102887f6ce600d092675bf3528a-0'
+    }
+    withName: '.*:BOWTIE2_ALIGN_TRIMMED' {
+        container = 'quay.io/biocontainers/mulled-v2-ac74a7f02cebcfcc07d8e8d1d750af9c83b4d45a:a0ffedb52808e102887f6ce600d092675bf3528a-0'
+    }
+    withName: '.*:BUILD_CONTACT_MAPS' {
+        container = 'quay.io/nf-core/ubuntu:20.04'
+    }
+    withName: '.*:COMBINE_MATES' {
+        container = 'quay.io/biocontainers/mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483:713df51cd897ceb893b9a6e6420f527d83c2ed95-0'
+    }
+    withName: '.*:COOLTOOLS_EIGSCIS' {
+        container = 'quay.io/biocontainers/mulled-v2-c81d8d6b6acf4714ffaae1a274527a41958443f6:cc7ea58b8cefc76bed985dcfe261cb276ed9e0cf-0'
+    }
+    withName: '.*:GET_RESTRICTION_FRAGMENTS' {
+        container = 'quay.io/biocontainers/mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483:713df51cd897ceb893b9a6e6420f527d83c2ed95-0'
+    }
+    withName: '.*:GET_VALID_INTERACTION' {
+        container = 'quay.io/biocontainers/mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483:713df51cd897ceb893b9a6e6420f527d83c2ed95-0'
+    }
+    withName: '.*:GET_VALID_INTERACTION_DNASE' {
+        container = 'quay.io/biocontainers/mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483:713df51cd897ceb893b9a6e6420f527d83c2ed95-0'
+    }
+    withName: '.*:ICE_NORMALIZATION' {
+        container = 'quay.io/biocontainers/mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483:713df51cd897ceb893b9a6e6420f527d83c2ed95-0'
+    }
+    withName: '.*:MERGE_STATS' {
+        container = 'quay.io/biocontainers/mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483:713df51cd897ceb893b9a6e6420f527d83c2ed95-0'
+    }
+    withName: '.*:MERGE_VALID_INTERACTION' {
+        container = 'quay.io/nf-core/ubuntu:20.04'
+    }
+    withName: '.*:SAMPLESHEET_CHECK' {
+        container = 'quay.io/biocontainers/python:3.8.3'
+    }
+    withName: '.*:SPLIT_COOLER_DUMP' {
+        container = 'quay.io/nf-core/ubuntu:20.04'
+    }
+    withName: '.*:TRIM_READS' {
+        container = 'quay.io/nf-core/ubuntu:20.04'
+    }
+}

modules/local/hicpro/run_ice.nf

-process ICE_NORMALIZATION{
+process ICE_NORMALIZATION {
     tag "$meta.id"
     label 'process_high_memory'
 
     conda "conda-forge::python=3.9 bioconda::iced=0.5.10 conda-forge::numpy=1.22.3"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483:713df51cd897ceb893b9a6e6420f527d83c2ed95-0' :
-        'biocontainers/mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483:713df51cd897ceb893b9a6e6420f527d83c2ed95-0'}"
+        'biocontainers/mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483:713df51cd897ceb893b9a6e6420f527d83c2ed95-0' }"
 
     input:
     tuple val(meta), val(res), path(rmaps), path(bed)

nextflow.config

@@ -215,6 +215,9 @@ profiles {
         executor.cpus          = 16
         executor.memory        = 60.GB
     }
+    public_aws_ecr {
+        includeConfig 'conf/public_aws_ecr.config'
+    }
     test      { includeConfig 'conf/test.config'      }
     test_full { includeConfig 'conf/test_full.config' }
 }