From bc1985b1e6e3dd1a7ec1256df8327ee0b89f4b5a Mon Sep 17 00:00:00 2001 From: maxulysse Date: Wed, 7 Jun 2023 19:31:08 +0200 Subject: [PATCH 1/4] patch more modules --- CHANGELOG.md | 2 ++ modules.json | 10 +++++----- modules/nf-core/deepvariant/main.nf | 2 +- modules/nf-core/gatk4/applybqsrspark/main.nf | 2 +- modules/nf-core/gatk4/baserecalibratorspark/main.nf | 2 +- modules/nf-core/gatk4/cnnscorevariants/main.nf | 2 +- modules/nf-core/gatk4/markduplicatesspark/main.nf | 2 +- 7 files changed, 12 insertions(+), 10 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 95f89562b..657580cce 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 +- [#1082](https://github.com/nf-core/sarek/pull/1082) - Patch more modules to use quay.io registry + ### Removed ## [3.2.0](https://github.com/nf-core/sarek/releases/tag/3.2.0) - Bierikjávrre diff --git a/modules.json b/modules.json index 8dbf98e63..ede849ff9 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 2cea90ab9..1a24ba34b 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 e920a2554..88ead471c 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 8857dbc38..d240a10d3 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 730544f61..5e843ce6c 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 d1388298c..f64fbfd52 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) From 382b1f925a97c8c2c1390ff1dfd29f895dbb2f22 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Wed, 7 Jun 2023 20:43:37 +0200 Subject: [PATCH 2/4] update public _aws_ecr profile --- CHANGELOG.md | 1 + conf/public_aws_ecr.config | 15 +++++++++++++++ 2 files changed, 16 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 3a4453d3a..02f17472a 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -18,6 +18,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [#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 ### Removed diff --git a/conf/public_aws_ecr.config b/conf/public_aws_ecr.config index a1445ebed..335909060 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' } From 0952e294cb36d58fd68377f516c9729b503ca2be Mon Sep 17 00:00:00 2001 From: maxulysse Date: Wed, 7 Jun 2023 21:18:52 +0200 Subject: [PATCH 3/4] add registry for singularity --- CHANGELOG.md | 1 + nextflow.config | 9 +++++---- 2 files changed, 6 insertions(+), 4 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 02f17472a..abfff0b66 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -19,6 +19,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [#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 ### Removed diff --git a/nextflow.config b/nextflow.config index b5189ecf5..204f94ce6 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 { From 3bcc1040a1023286e115298313acea20376d31ce Mon Sep 17 00:00:00 2001 From: maxulysse Date: Wed, 7 Jun 2023 22:00:16 +0200 Subject: [PATCH 4/4] nf-core bump-version -n 23.04.0 --- .github/workflows/ci.yml | 2 +- .github/workflows/pytest-workflow.yml | 2 +- CHANGELOG.md | 2 ++ README.md | 2 +- nextflow.config | 2 +- 5 files changed, 6 insertions(+), 4 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index b97b8b5d6..743876c1e 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 8b6f9d2cc..394802985 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 abfff0b66..2d8c95a74 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -13,6 +13,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### Changed +- [#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 diff --git a/README.md b/README.md index eba6b6ab2..370f3557a 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/nextflow.config b/nextflow.config index 204f94ce6..dafabcfca 100644 --- a/nextflow.config +++ b/nextflow.config @@ -322,7 +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 = '3.3dev' doi = '10.12688/f1000research.16665.2, 10.5281/zenodo.4063683' }