From 6ec32edc36f9fe02951d0e5ca7c978d6fb99bfa1 Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Thu, 10 Apr 2025 13:04:00 +0200 Subject: [PATCH 01/10] bump nf-schema to 2.4.0 --- CHANGELOG.md | 2 ++ nf_core/pipeline-template/nextflow.config | 4 ++-- tmp/pytest-of-nvnieuwk/pytest-2/test_github_details0 | 1 + tmp/pytest-of-nvnieuwk/pytest-2/test_github_exit_message0 | 1 + tmp/pytest-of-nvnieuwk/pytest-2/test_github_question0 | 1 + 5 files changed, 7 insertions(+), 2 deletions(-) create mode 160000 tmp/pytest-of-nvnieuwk/pytest-2/test_github_details0 create mode 160000 tmp/pytest-of-nvnieuwk/pytest-2/test_github_exit_message0 create mode 160000 tmp/pytest-of-nvnieuwk/pytest-2/test_github_question0 diff --git a/CHANGELOG.md b/CHANGELOG.md index c2c92c6526..534a9fbc43 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -11,6 +11,8 @@ - Run awsfulltest after release, and with dev revision on PRs to master ([#3485](https://github.com/nf-core/tools/pull/3485)) - Add .nftignore to trigger list ([#3508](https://github.com/nf-core/tools/pull/3508)) - Include the centralized nf-core configs also in offline mode, if a local copy is available. ([#3491](https://github.com/nf-core/tools/pull/3491)) +- Bump nf-schema to `2.4.0` +- Bump the minimal Nextflow version to `24.10.0` ### Linting diff --git a/nf_core/pipeline-template/nextflow.config b/nf_core/pipeline-template/nextflow.config index 67ae0769bc..9d173e72d2 100644 --- a/nf_core/pipeline-template/nextflow.config +++ b/nf_core/pipeline-template/nextflow.config @@ -291,7 +291,7 @@ manifest { description = """{{ description }}""" mainScript = 'main.nf' defaultBranch = '{{ default_branch }}' - nextflowVersion = '!>=24.04.2' + nextflowVersion = '!>=24.04.10' version = '{{ version }}' doi = '' } @@ -299,7 +299,7 @@ manifest { {% if nf_schema -%} // Nextflow plugins plugins { - id 'nf-schema@2.3.0' // Validation of pipeline parameters and creation of an input channel from a sample sheet + id 'nf-schema@2.4.0' // Validation of pipeline parameters and creation of an input channel from a sample sheet } validation { diff --git a/tmp/pytest-of-nvnieuwk/pytest-2/test_github_details0 b/tmp/pytest-of-nvnieuwk/pytest-2/test_github_details0 new file mode 160000 index 0000000000..e5415773b8 --- /dev/null +++ b/tmp/pytest-of-nvnieuwk/pytest-2/test_github_details0 @@ -0,0 +1 @@ +Subproject commit e5415773b896a7538d8a3fb6b4526b91f9abc819 diff --git a/tmp/pytest-of-nvnieuwk/pytest-2/test_github_exit_message0 b/tmp/pytest-of-nvnieuwk/pytest-2/test_github_exit_message0 new file mode 160000 index 0000000000..9184399240 --- /dev/null +++ b/tmp/pytest-of-nvnieuwk/pytest-2/test_github_exit_message0 @@ -0,0 +1 @@ +Subproject commit 9184399240ac8946be6d595df0fbbe70543d9f8a diff --git a/tmp/pytest-of-nvnieuwk/pytest-2/test_github_question0 b/tmp/pytest-of-nvnieuwk/pytest-2/test_github_question0 new file mode 160000 index 0000000000..9b90b3a2f6 --- /dev/null +++ b/tmp/pytest-of-nvnieuwk/pytest-2/test_github_question0 @@ -0,0 +1 @@ +Subproject commit 9b90b3a2f6362fec69241460d74b1e7fb74f3a8e From 3c21928f24fe3d6db79145b72bd72bcd35bee398 Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Thu, 10 Apr 2025 13:05:18 +0200 Subject: [PATCH 02/10] add PR number to changelog --- CHANGELOG.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 534a9fbc43..828360bfb8 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -11,8 +11,8 @@ - Run awsfulltest after release, and with dev revision on PRs to master ([#3485](https://github.com/nf-core/tools/pull/3485)) - Add .nftignore to trigger list ([#3508](https://github.com/nf-core/tools/pull/3508)) - Include the centralized nf-core configs also in offline mode, if a local copy is available. ([#3491](https://github.com/nf-core/tools/pull/3491)) -- Bump nf-schema to `2.4.0` -- Bump the minimal Nextflow version to `24.10.0` +- Bump nf-schema to `2.4.0` ([#3533](https://github.com/nf-core/tools/pull/3533)) +- Bump the minimal Nextflow version to `24.10.0` ([#3533](https://github.com/nf-core/tools/pull/3533)) ### Linting From a628c8e535641e0fe82035cbc37556f035ebec8e Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Thu, 10 Apr 2025 13:11:05 +0200 Subject: [PATCH 03/10] remove tmp files --- tmp/pytest-of-nvnieuwk/pytest-2/test_github_details0 | 1 - tmp/pytest-of-nvnieuwk/pytest-2/test_github_exit_message0 | 1 - tmp/pytest-of-nvnieuwk/pytest-2/test_github_question0 | 1 - 3 files changed, 3 deletions(-) delete mode 160000 tmp/pytest-of-nvnieuwk/pytest-2/test_github_details0 delete mode 160000 tmp/pytest-of-nvnieuwk/pytest-2/test_github_exit_message0 delete mode 160000 tmp/pytest-of-nvnieuwk/pytest-2/test_github_question0 diff --git a/tmp/pytest-of-nvnieuwk/pytest-2/test_github_details0 b/tmp/pytest-of-nvnieuwk/pytest-2/test_github_details0 deleted file mode 160000 index e5415773b8..0000000000 --- a/tmp/pytest-of-nvnieuwk/pytest-2/test_github_details0 +++ /dev/null @@ -1 +0,0 @@ -Subproject commit e5415773b896a7538d8a3fb6b4526b91f9abc819 diff --git a/tmp/pytest-of-nvnieuwk/pytest-2/test_github_exit_message0 b/tmp/pytest-of-nvnieuwk/pytest-2/test_github_exit_message0 deleted file mode 160000 index 9184399240..0000000000 --- a/tmp/pytest-of-nvnieuwk/pytest-2/test_github_exit_message0 +++ /dev/null @@ -1 +0,0 @@ -Subproject commit 9184399240ac8946be6d595df0fbbe70543d9f8a diff --git a/tmp/pytest-of-nvnieuwk/pytest-2/test_github_question0 b/tmp/pytest-of-nvnieuwk/pytest-2/test_github_question0 deleted file mode 160000 index 9b90b3a2f6..0000000000 --- a/tmp/pytest-of-nvnieuwk/pytest-2/test_github_question0 +++ /dev/null @@ -1 +0,0 @@ -Subproject commit 9b90b3a2f6362fec69241460d74b1e7fb74f3a8e From 3cb6cb05db126e738dc61b66160a478f58a261a5 Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Thu, 10 Apr 2025 13:12:00 +0200 Subject: [PATCH 04/10] fix lint tests --- nf_core/pipeline-template/.github/workflows/nf-test.yml | 2 +- nf_core/pipeline-template/README.md | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/nf_core/pipeline-template/.github/workflows/nf-test.yml b/nf_core/pipeline-template/.github/workflows/nf-test.yml index dd59786d56..b04a47966c 100644 --- a/nf_core/pipeline-template/.github/workflows/nf-test.yml +++ b/nf_core/pipeline-template/.github/workflows/nf-test.yml @@ -91,7 +91,7 @@ jobs: - isMain: false profile: "singularity" NXF_VER: - - "24.04.2" + - "24.10.0" - "latest-everything" env: NXF_ANSI_LOG: false diff --git a/nf_core/pipeline-template/README.md b/nf_core/pipeline-template/README.md index 1db8724a35..c83c1e0536 100644 --- a/nf_core/pipeline-template/README.md +++ b/nf_core/pipeline-template/README.md @@ -20,7 +20,7 @@ [![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX) [![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com) -[![Nextflow](https://img.shields.io/badge/version-%E2%89%A524.04.2-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/) +[![Nextflow](https://img.shields.io/badge/version-%E2%89%A524.10.0-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/) [![nf-core template version](https://img.shields.io/badge/nf--core_template-{{ nf_core_version }}-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/{{ nf_core_version }}) [![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/) From aaa435904b0c8eeac71ab84445c700531e20231e Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Thu, 10 Apr 2025 13:15:07 +0200 Subject: [PATCH 05/10] update ci nextflow version of tools --- .github/workflows/create-lint-wf.yml | 2 +- .github/workflows/create-test-wf.yml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/create-lint-wf.yml b/.github/workflows/create-lint-wf.yml index 997ad084a9..62693be089 100644 --- a/.github/workflows/create-lint-wf.yml +++ b/.github/workflows/create-lint-wf.yml @@ -38,7 +38,7 @@ jobs: strategy: matrix: NXF_VER: - - "24.04.2" + - "24.10.0" - "latest-everything" steps: - name: go to subdirectory and change nextflow workdir diff --git a/.github/workflows/create-test-wf.yml b/.github/workflows/create-test-wf.yml index 1166bc0107..67a3399972 100644 --- a/.github/workflows/create-test-wf.yml +++ b/.github/workflows/create-test-wf.yml @@ -39,7 +39,7 @@ jobs: strategy: matrix: NXF_VER: - - "24.04.2" + - "24.10.0" - "latest-everything" steps: - name: go to working directory From 88c29ff96df241e47d4d2a3b2fcbc0489f892bbb Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Thu, 10 Apr 2025 13:20:25 +0200 Subject: [PATCH 06/10] fix version typo --- nf_core/pipeline-template/nextflow.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nf_core/pipeline-template/nextflow.config b/nf_core/pipeline-template/nextflow.config index 9d173e72d2..416f8de6b8 100644 --- a/nf_core/pipeline-template/nextflow.config +++ b/nf_core/pipeline-template/nextflow.config @@ -291,7 +291,7 @@ manifest { description = """{{ description }}""" mainScript = 'main.nf' defaultBranch = '{{ default_branch }}' - nextflowVersion = '!>=24.04.10' + nextflowVersion = '!>=24.10.0' version = '{{ version }}' doi = '' } From 63a31c40333d8175e6842365e88888fa6447613a Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com> Date: Thu, 10 Apr 2025 15:09:52 +0200 Subject: [PATCH 07/10] Update CHANGELOG.md Co-authored-by: Maxime U Garcia --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 828360bfb8..d576996b4e 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -11,7 +11,7 @@ - Run awsfulltest after release, and with dev revision on PRs to master ([#3485](https://github.com/nf-core/tools/pull/3485)) - Add .nftignore to trigger list ([#3508](https://github.com/nf-core/tools/pull/3508)) - Include the centralized nf-core configs also in offline mode, if a local copy is available. ([#3491](https://github.com/nf-core/tools/pull/3491)) -- Bump nf-schema to `2.4.0` ([#3533](https://github.com/nf-core/tools/pull/3533)) +- Bump nf-schema to `2.4.1` ([#3533](https://github.com/nf-core/tools/pull/3533)) - Bump the minimal Nextflow version to `24.10.0` ([#3533](https://github.com/nf-core/tools/pull/3533)) ### Linting From 4e31eb4e58a7997818d3f15b4f7747b11d9a85f4 Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com> Date: Thu, 10 Apr 2025 15:09:57 +0200 Subject: [PATCH 08/10] Update nf_core/pipeline-template/nextflow.config Co-authored-by: Maxime U Garcia --- nf_core/pipeline-template/nextflow.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nf_core/pipeline-template/nextflow.config b/nf_core/pipeline-template/nextflow.config index 416f8de6b8..cf738401df 100644 --- a/nf_core/pipeline-template/nextflow.config +++ b/nf_core/pipeline-template/nextflow.config @@ -299,7 +299,7 @@ manifest { {% if nf_schema -%} // Nextflow plugins plugins { - id 'nf-schema@2.4.0' // Validation of pipeline parameters and creation of an input channel from a sample sheet + id 'nf-schema@2.4.1' // Validation of pipeline parameters and creation of an input channel from a sample sheet } validation { From 2c63d91236d0f5edb02605702def5e2ffc0c955b Mon Sep 17 00:00:00 2001 From: mashehu Date: Tue, 17 Jun 2025 17:23:30 +0200 Subject: [PATCH 09/10] bump to nf-schema 2.4.2 and nextflow to 24.10.8 --- .github/snapshots/default.nf.test.snap | 2 +- .github/workflows/create-lint-wf.yml | 2 +- .github/workflows/create-test-wf.yml | 2 +- CHANGELOG.md | 4 ++-- nf_core/pipeline-template/.github/workflows/nf-test.yml | 2 +- nf_core/pipeline-template/README.md | 2 +- .../modules/nf-core/multiqc/tests/main.nf.test.snap | 6 +++--- nf_core/pipeline-template/nextflow.config | 4 ++-- .../nf-core/utils_nfschema_plugin/tests/nextflow.config | 2 +- nf_core/pipelines/lint/readme.py | 2 +- 10 files changed, 14 insertions(+), 14 deletions(-) diff --git a/.github/snapshots/default.nf.test.snap b/.github/snapshots/default.nf.test.snap index a5b17b4f16..baa9ba23cb 100644 --- a/.github/snapshots/default.nf.test.snap +++ b/.github/snapshots/default.nf.test.snap @@ -109,7 +109,7 @@ ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.4" + "nextflow": "24.10.8" }, "timestamp": "2025-05-07T13:29:04.284923" } diff --git a/.github/workflows/create-lint-wf.yml b/.github/workflows/create-lint-wf.yml index e22e49c934..d2374d4542 100644 --- a/.github/workflows/create-lint-wf.yml +++ b/.github/workflows/create-lint-wf.yml @@ -32,7 +32,7 @@ jobs: strategy: matrix: NXF_VER: - - "24.10.0" + - "24.10.8" - "latest-everything" steps: - name: go to subdirectory and change nextflow workdir diff --git a/.github/workflows/create-test-wf.yml b/.github/workflows/create-test-wf.yml index a1b8d2fbea..55af47a8cf 100644 --- a/.github/workflows/create-test-wf.yml +++ b/.github/workflows/create-test-wf.yml @@ -32,7 +32,7 @@ jobs: strategy: matrix: NXF_VER: - - "24.10.0" + - "24.10.8" - "latest-everything" steps: - name: go to working directory diff --git a/CHANGELOG.md b/CHANGELOG.md index 14c0f4bf83..090d6a67ae 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -6,8 +6,8 @@ - Avoid overriding `NFT_DIFF` and `NFT_DIFF_ARGS` in `nf-test` action ([#3606](https://github.com/nf-core/tools/pull/3606)) and ([#3619](https://github.com/nf-core/tools/pull/3619)) - fix nf-test scope to ignore nf-core module/swf tests ([#3609](https://github.com/nf-core/tools/pull/3609)) -- Bump nf-schema to `2.4.1` ([#3533](https://github.com/nf-core/tools/pull/3533)) -- Bump the minimal Nextflow version to `24.10.0` ([#3533](https://github.com/nf-core/tools/pull/3533)) +- Bump nf-schema to `2.4.2` ([#3533](https://github.com/nf-core/tools/pull/3533)) +- Bump the minimal Nextflow version to `24.10.8` ([#3533](https://github.com/nf-core/tools/pull/3533)) ### Linting diff --git a/nf_core/pipeline-template/.github/workflows/nf-test.yml b/nf_core/pipeline-template/.github/workflows/nf-test.yml index 55ebb110ac..ed3cd87a55 100644 --- a/nf_core/pipeline-template/.github/workflows/nf-test.yml +++ b/nf_core/pipeline-template/.github/workflows/nf-test.yml @@ -87,7 +87,7 @@ jobs: - isMain: false profile: "singularity" NXF_VER: - - "24.10.0" + - "24.10.8" - "latest-everything" env: NXF_ANSI_LOG: false diff --git a/nf_core/pipeline-template/README.md b/nf_core/pipeline-template/README.md index c83c1e0536..9a91ddea40 100644 --- a/nf_core/pipeline-template/README.md +++ b/nf_core/pipeline-template/README.md @@ -20,7 +20,7 @@ [![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX) [![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com) -[![Nextflow](https://img.shields.io/badge/version-%E2%89%A524.10.0-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/) +[![Nextflow](https://img.shields.io/badge/version-%E2%89%A524.10.8-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/) [![nf-core template version](https://img.shields.io/badge/nf--core_template-{{ nf_core_version }}-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/{{ nf_core_version }}) [![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/) diff --git a/nf_core/pipeline-template/modules/nf-core/multiqc/tests/main.nf.test.snap b/nf_core/pipeline-template/modules/nf-core/multiqc/tests/main.nf.test.snap index 7b7c132205..ae3c18576e 100644 --- a/nf_core/pipeline-template/modules/nf-core/multiqc/tests/main.nf.test.snap +++ b/nf_core/pipeline-template/modules/nf-core/multiqc/tests/main.nf.test.snap @@ -7,7 +7,7 @@ ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.4" + "nextflow": "24.10.8" }, "timestamp": "2025-01-27T09:29:57.631982377" }, @@ -22,7 +22,7 @@ ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.4" + "nextflow": "24.10.8" }, "timestamp": "2025-01-27T09:30:34.743726958" }, @@ -34,7 +34,7 @@ ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.4" + "nextflow": "24.10.8" }, "timestamp": "2025-01-27T09:30:21.44383553" } diff --git a/nf_core/pipeline-template/nextflow.config b/nf_core/pipeline-template/nextflow.config index a44018a5a6..a24ddec186 100644 --- a/nf_core/pipeline-template/nextflow.config +++ b/nf_core/pipeline-template/nextflow.config @@ -298,7 +298,7 @@ manifest { description = """{{ description }}""" mainScript = 'main.nf' defaultBranch = '{{ default_branch }}' - nextflowVersion = '!>=24.10.0' + nextflowVersion = '!>=24.10.8' version = '{{ version }}' doi = '' } @@ -306,7 +306,7 @@ manifest { {% if nf_schema -%} // Nextflow plugins plugins { - id 'nf-schema@2.4.1' // Validation of pipeline parameters and creation of an input channel from a sample sheet + id 'nf-schema@2.4.2' // Validation of pipeline parameters and creation of an input channel from a sample sheet } validation { diff --git a/nf_core/pipeline-template/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config b/nf_core/pipeline-template/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config index 0907ac58f0..09ef842aef 100644 --- a/nf_core/pipeline-template/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config +++ b/nf_core/pipeline-template/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config @@ -1,5 +1,5 @@ plugins { - id "nf-schema@2.1.0" + id "nf-schema@2.4.2" } validation { diff --git a/nf_core/pipelines/lint/readme.py b/nf_core/pipelines/lint/readme.py index 0cdd52744d..0addbebfea 100644 --- a/nf_core/pipelines/lint/readme.py +++ b/nf_core/pipelines/lint/readme.py @@ -53,7 +53,7 @@ def readme(self): if "nextflow_badge" not in ignore_configs: # Check that there is a readme badge showing the minimum required version of Nextflow - # [![Nextflow](https://img.shields.io/badge/version-%E2%89%A524.04.2-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/) + # [![Nextflow](https://img.shields.io/badge/version-%E2%89%A524.10.8-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/) # and that it has the correct version nf_badge_re = r"\[!\[Nextflow\]\(https://img\.shields\.io/badge/version-!?(?:%E2%89%A5|%3E%3D)([\d\.]+)-green\?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow\.io\)\]\(https://www\.nextflow\.io/\)" match = re.search(nf_badge_re, content) From d70172c33a6c07a85a415ef14d4fa845d82f721b Mon Sep 17 00:00:00 2001 From: mashehu Date: Tue, 17 Jun 2025 17:25:42 +0200 Subject: [PATCH 10/10] remove deprecated author field from nextflow.config --- nf_core/pipeline-template/nextflow.config | 1 - nf_core/pipelines/lint/files_unchanged.py | 3 ++- nf_core/pipelines/sync.py | 3 ++- 3 files changed, 4 insertions(+), 3 deletions(-) diff --git a/nf_core/pipeline-template/nextflow.config b/nf_core/pipeline-template/nextflow.config index a24ddec186..17df89bcad 100644 --- a/nf_core/pipeline-template/nextflow.config +++ b/nf_core/pipeline-template/nextflow.config @@ -280,7 +280,6 @@ dag { manifest { name = '{{ name }}' - author = """{{ author }}""" // The author field is deprecated from Nextflow version 24.10.0, use contributors instead contributors = [ // TODO nf-core: Update the field with the details of the contributors to your pipeline. New with Nextflow version 24.10.0 {%- for author_name in author.split(",") %} diff --git a/nf_core/pipelines/lint/files_unchanged.py b/nf_core/pipelines/lint/files_unchanged.py index 464ce00ed6..a48a3d54e3 100644 --- a/nf_core/pipelines/lint/files_unchanged.py +++ b/nf_core/pipelines/lint/files_unchanged.py @@ -72,7 +72,8 @@ def files_unchanged(self) -> dict[str, Union[list[str], bool]]: required_pipeline_config = { "manifest.name", "manifest.description", - } # TODO: add "manifest.contributors" when minimum nextflow version is >=24.10.0 + "manifest.contributors", + } missing_pipeline_config = required_pipeline_config.difference(self.nf_config) if missing_pipeline_config: return {"ignored": [f"Required pipeline config not found - {missing_pipeline_config}"]} diff --git a/nf_core/pipelines/sync.py b/nf_core/pipelines/sync.py index 06b770e598..736d7d35da 100644 --- a/nf_core/pipelines/sync.py +++ b/nf_core/pipelines/sync.py @@ -85,7 +85,8 @@ def __init__( "manifest.name", "manifest.description", "manifest.version", - ] # TODO: add "manifest.contributors" when minimum nextflow version is >=24.10.0 + "manifest.contributors", + ] self.force_pr = force_pr self.gh_username = gh_username