diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index b97b8b5d63..743876c1eb 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -23,7 +23,7 @@ jobs: fail-fast: false matrix: NXF_VER: - - "22.10.1" + - "23.04.0" - "latest-everything" test: - "default" diff --git a/.github/workflows/pytest-workflow.yml b/.github/workflows/pytest-workflow.yml index 8b6f9d2ccc..394802985f 100644 --- a/.github/workflows/pytest-workflow.yml +++ b/.github/workflows/pytest-workflow.yml @@ -37,7 +37,7 @@ jobs: TEST_DATA_BASE: - "test-datasets/data" NXF_VER: - - "22.10.1" + - "23.04.0" - "latest-everything" exclude: # - profile: "conda" diff --git a/CHANGELOG.md b/CHANGELOG.md index b29051f702..9d6e98f019 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -13,11 +13,15 @@ Pierikjaure is a previous spelling of Bierikjávrre. - [#1073](https://github.com/nf-core/sarek/pull/1073) - Back to dev - [#1080](https://github.com/nf-core/sarek/pull/1080) - Prepare release `3.2.1` +- [#1082](https://github.com/nf-core/sarek/pull/1082) - Bump minimal Nextflow version to 23.04.0 ### Fixed - [#1078](https://github.com/nf-core/sarek/pull/1078) - Update tabix/bgziptabix module to fix typo - [#1079](https://github.com/nf-core/sarek/pull/1079) - Fixed typo in profile name for tower aws megatests +- [#1082](https://github.com/nf-core/sarek/pull/1082) - Patch more modules to use quay.io registry +- [#1082](https://github.com/nf-core/sarek/pull/1082) - Update `public_aws_ecr` profile +- [#1082](https://github.com/nf-core/sarek/pull/1082) - Add quay.io as singularity default registry ## [3.2.0](https://github.com/nf-core/sarek/releases/tag/3.2.0) - Bierikjávrre diff --git a/README.md b/README.md index eba6b6ab2f..370f3557a8 100644 --- a/README.md +++ b/README.md @@ -7,7 +7,7 @@ [![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/sarek/results) [![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.3476426-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.3476425) -[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A522.10.1-23aa62.svg)](https://www.nextflow.io/) +[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A523.04.0-23aa62.svg)](https://www.nextflow.io/) [![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/) [![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/) [![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/) diff --git a/conf/public_aws_ecr.config b/conf/public_aws_ecr.config index a1445ebed8..335909060a 100644 --- a/conf/public_aws_ecr.config +++ b/conf/public_aws_ecr.config @@ -39,9 +39,24 @@ process { 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' } diff --git a/modules.json b/modules.json index e1f9fcede1..3e59e23517 100644 --- a/modules.json +++ b/modules.json @@ -107,7 +107,7 @@ }, "deepvariant": { "branch": "master", - "git_sha": "0460d316170f75f323111b4a2c0a2989f0c32013", + "git_sha": "4b7d4863a5883b76e6bff13b6e52468fab090c5b", "installed_by": ["modules"] }, "dragmap/align": { @@ -168,7 +168,7 @@ }, "gatk4/applybqsrspark": { "branch": "master", - "git_sha": "b9829e1064382745d8dff7f1d74d2138d2864f71", + "git_sha": "4b7d4863a5883b76e6bff13b6e52468fab090c5b", "installed_by": ["modules"] }, "gatk4/applyvqsr": { @@ -183,7 +183,7 @@ }, "gatk4/baserecalibratorspark": { "branch": "master", - "git_sha": "b9829e1064382745d8dff7f1d74d2138d2864f71", + "git_sha": "4b7d4863a5883b76e6bff13b6e52468fab090c5b", "installed_by": ["modules"] }, "gatk4/calculatecontamination": { @@ -193,7 +193,7 @@ }, "gatk4/cnnscorevariants": { "branch": "master", - "git_sha": "b9829e1064382745d8dff7f1d74d2138d2864f71", + "git_sha": "4b7d4863a5883b76e6bff13b6e52468fab090c5b", "installed_by": ["modules"] }, "gatk4/createsequencedictionary": { @@ -263,7 +263,7 @@ }, "gatk4/markduplicatesspark": { "branch": "master", - "git_sha": "b9829e1064382745d8dff7f1d74d2138d2864f71", + "git_sha": "4b7d4863a5883b76e6bff13b6e52468fab090c5b", "installed_by": ["modules"] }, "gatk4/mergemutectstats": { diff --git a/modules/nf-core/deepvariant/main.nf b/modules/nf-core/deepvariant/main.nf index 2cea90ab9b..1a24ba34b8 100644 --- a/modules/nf-core/deepvariant/main.nf +++ b/modules/nf-core/deepvariant/main.nf @@ -2,7 +2,7 @@ process DEEPVARIANT { tag "$meta.id" label 'process_high' - container "docker.io/google/deepvariant:1.5.0" + container "nf-core/deepvariant:1.5.0" // Exit if running this module with -profile conda / -profile mamba if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { diff --git a/modules/nf-core/gatk4/applybqsrspark/main.nf b/modules/nf-core/gatk4/applybqsrspark/main.nf index e920a2554d..88ead471c8 100644 --- a/modules/nf-core/gatk4/applybqsrspark/main.nf +++ b/modules/nf-core/gatk4/applybqsrspark/main.nf @@ -3,7 +3,7 @@ process GATK4_APPLYBQSR_SPARK { label 'process_low' conda "bioconda::gatk4=4.3.0.0 conda-forge::openjdk=8.0.312" - container 'docker.io/broadinstitute/gatk:4.4.0.0' + container "nf-core/gatk:4.4.0.0" input: tuple val(meta), path(input), path(input_index), path(bqsr_table), path(intervals) diff --git a/modules/nf-core/gatk4/baserecalibratorspark/main.nf b/modules/nf-core/gatk4/baserecalibratorspark/main.nf index 8857dbc382..d240a10d3f 100644 --- a/modules/nf-core/gatk4/baserecalibratorspark/main.nf +++ b/modules/nf-core/gatk4/baserecalibratorspark/main.nf @@ -3,7 +3,7 @@ process GATK4_BASERECALIBRATOR_SPARK { label 'process_low' conda "bioconda::gatk4=4.4.0.0 conda-forge::openjdk=8.0.312" - container 'docker.io/broadinstitute/gatk:4.4.0.0' + container "nf-core/gatk:4.4.0.0" input: tuple val(meta), path(input), path(input_index), path(intervals) diff --git a/modules/nf-core/gatk4/cnnscorevariants/main.nf b/modules/nf-core/gatk4/cnnscorevariants/main.nf index 730544f61e..5e843ce6c6 100644 --- a/modules/nf-core/gatk4/cnnscorevariants/main.nf +++ b/modules/nf-core/gatk4/cnnscorevariants/main.nf @@ -3,7 +3,7 @@ process GATK4_CNNSCOREVARIANTS { label 'process_low' //Conda is not supported at the moment: https://github.com/broadinstitute/gatk/issues/7811 - container "docker.io/broadinstitute/gatk:4.4.0.0" //Biocontainers is missing a package + container "nf-core/gatk:4.4.0.0" //Biocontainers is missing a package // Exit if running this module with -profile conda / -profile mamba if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { diff --git a/modules/nf-core/gatk4/markduplicatesspark/main.nf b/modules/nf-core/gatk4/markduplicatesspark/main.nf index d1388298c1..f64fbfd521 100644 --- a/modules/nf-core/gatk4/markduplicatesspark/main.nf +++ b/modules/nf-core/gatk4/markduplicatesspark/main.nf @@ -3,7 +3,7 @@ process GATK4_MARKDUPLICATES_SPARK { label 'process_high' conda "bioconda::gatk4=4.3.0.0 conda-forge::openjdk=8.0.312" - container 'docker.io/broadinstitute/gatk:4.4.0.0' + container "nf-core/gatk:4.4.0.0" input: tuple val(meta), path(bam) diff --git a/nextflow.config b/nextflow.config index 6ebf0db79b..8d0dd50a29 100644 --- a/nextflow.config +++ b/nextflow.config @@ -291,11 +291,12 @@ env { // Capture exit codes from upstream processes when piping process.shell = ['/bin/bash', '-euo', 'pipefail'] -// Set default registry for Docker and Podman independent of -profile -// Will not be used unless Docker / Podman are enabled +// Set default registry for Docker, Singularity and Podman independent of -profile +// Will not be used unless Docker, Singularity and Podman are enabled // Set to your registry if you have a mirror of containers -docker.registry = 'quay.io' -podman.registry = 'quay.io' +docker.registry = 'quay.io' +podman.registry = 'quay.io' +singularity.registry = 'quay.io' def trace_timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss') timeline { @@ -321,7 +322,7 @@ manifest { homePage = 'https://github.com/nf-core/sarek' description = """An open-source analysis pipeline to detect germline or somatic variants from whole genome or targeted sequencing""" mainScript = 'main.nf' - nextflowVersion = '!>=22.10.1' + nextflowVersion = '!>=23.04.0' version = '3.2.1' doi = '10.12688/f1000research.16665.2, 10.5281/zenodo.4063683' }