diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml index ad7e2ddfdff0e494d19ce8baa49db8123d6728a6..2b99a42b8738de2bf1f214c5f3d267915b5178ac 100644 --- a/.github/workflows/awsfulltest.yml +++ b/.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 diff --git a/.github/workflows/awstest.yml b/.github/workflows/awstest.yml index 3f9b365ffe5729722f94316715fe5e654860c152..177543c03385b4a9528124d6fb2ee6b995f6ac33 100644 --- a/.github/workflows/awstest.yml +++ b/.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 diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 5531e307166fc8f4d5717ba3efc646693560c67b..83b111b5d502d72f175c685c5af89e786a53b320 100644 --- a/.github/workflows/ci.yml +++ b/.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 }}" diff --git a/CHANGELOG.md b/CHANGELOG.md index 4095f4a54c775f1130bacd27a71a179b392315ae..ea99e6775dda65525ef2970bf0e4cd2a8bb7ba45 100644 --- a/CHANGELOG.md +++ b/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` diff --git a/conf/public_aws_ecr.config b/conf/public_aws_ecr.config new file mode 100644 index 0000000000000000000000000000000000000000..4979017e760018adb5923656635506aca6540012 --- /dev/null +++ b/conf/public_aws_ecr.config @@ -0,0 +1,57 @@ +/* +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 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' + } +} diff --git a/modules/local/hicpro/run_ice.nf b/modules/local/hicpro/run_ice.nf index 74c96dc828399461d725fc52752cf98337b5dc02..7ef5727378fdfabfb7b93e2852c11131481c0a11 100644 --- a/modules/local/hicpro/run_ice.nf +++ b/modules/local/hicpro/run_ice.nf @@ -1,11 +1,11 @@ -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) diff --git a/nextflow.config b/nextflow.config index 40507dd642c9a0dcd4fba6320ed5e750e1152445..931b861808632758b83c5a7ff6d411fed415ed79 100644 --- a/nextflow.config +++ b/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' } }