From 21c78e65f10fa87d7b81fb4990cde7931e96c535 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=BAlia=20Mir=20Pedrol?= Date: Fri, 22 Aug 2025 15:27:40 +0200 Subject: [PATCH 1/4] remove workflow.trace from nf-test snapshot to avoid errors due to incompatibility with nextflow --- nf_core/pipeline-template/tests/default.nf.test | 2 -- 1 file changed, 2 deletions(-) diff --git a/nf_core/pipeline-template/tests/default.nf.test b/nf_core/pipeline-template/tests/default.nf.test index a2eba5a782..8e463d2890 100644 --- a/nf_core/pipeline-template/tests/default.nf.test +++ b/nf_core/pipeline-template/tests/default.nf.test @@ -20,8 +20,6 @@ nextflow_pipeline { assertAll( { assert workflow.success}, { assert snapshot( - // Number of successful tasks - workflow.trace.succeeded().size(), // pipeline versions.yml file for multiqc from which Nextflow version is removed because we test pipelines on multiple Nextflow versions removeNextflowVersion("$outputDir/pipeline_info/{% if is_nfcore %}nf_core_{% endif %}{{ short_name }}_software_mqc_versions.yml"), // All stable path name, with a relative path From 2e2cb7af59bde1c0d8811050204d2ec187b1111b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=BAlia=20Mir=20Pedrol?= Date: Fri, 22 Aug 2025 15:27:57 +0200 Subject: [PATCH 2/4] remove requirements duplication --- requirements-dev.txt | 3 --- 1 file changed, 3 deletions(-) diff --git a/requirements-dev.txt b/requirements-dev.txt index 751f285412..840cb6d558 100644 --- a/requirements-dev.txt +++ b/requirements-dev.txt @@ -11,8 +11,6 @@ types-PyYAML types-requests types-jsonschema types-Markdown -types-PyYAML -types-requests types-setuptools typing_extensions >=4.0.0 pytest-asyncio @@ -20,4 +18,3 @@ pytest-textual-snapshot==1.1.0 pytest-workflow>=2.0.0 pytest-xdist>=3.7.0 pytest>=8.0.0 -ruff From 2c01ade5cf5a0c30af15d17ab1ebe726c9e9a697 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Fri, 22 Aug 2025 13:30:33 +0000 Subject: [PATCH 3/4] [automated] Update CHANGELOG.md --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index aa94d0f429..ea20118dc3 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -23,6 +23,7 @@ - Update python:3.13-slim Docker digest to 4c2cf99 ([#3700](https://github.com/nf-core/tools/pull/3700)) - Validation of meta.yaml in cross-org repos ([#3680](https://github.com/nf-core/tools/pull/3680)) - Replace arm profile with arm64 and emulate_amd64 profiles ([#3689](https://github.com/nf-core/tools/pull/3689)) +- Remove workflow.trace from nf-test snapshot ([#3721](https://github.com/nf-core/tools/pull/3721)) ## [v3.3.2 - Tungsten Tamarin Patch 2](https://github.com/nf-core/tools/releases/tag/3.3.2) - [2025-07-08] From 8086e729d7e34d43aa23a7c13092e6a4f4723ffc Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=BAlia=20Mir=20Pedrol?= Date: Fri, 22 Aug 2025 15:52:42 +0200 Subject: [PATCH 4/4] update all pipeline snapshots --- .github/snapshots/adaptivecard.nf.test.snap | 1 - .github/snapshots/changelog.nf.test.snap | 1 - .github/snapshots/ci.nf.test.snap | 1 - .github/snapshots/citations.nf.test.snap | 1 - .github/snapshots/code_linters.nf.test.snap | 1 - .github/snapshots/codespaces.nf.test.snap | 1 - .github/snapshots/default.nf.test.snap | 1 - .github/snapshots/documentation.nf.test.snap | 1 - .github/snapshots/email.nf.test.snap | 1 - .github/snapshots/fastqc.nf.test.snap | 1 - .github/snapshots/github_badges.nf.test.snap | 1 - .github/snapshots/gitpod.nf.test.snap | 1 - .github/snapshots/gpu.nf.test.snap | 1 - .github/snapshots/igenomes.nf.test.snap | 1 - .github/snapshots/license.nf.test.snap | 1 - .github/snapshots/modules.nf.test.snap | 1 - .github/snapshots/multiqc.nf.test.snap | 1 - .github/snapshots/nf_core_configs.nf.test.snap | 1 - .github/snapshots/nf_schema.nf.test.snap | 1 - .github/snapshots/rocrate.nf.test.snap | 1 - .github/snapshots/seqera_platform.nf.test.snap | 1 - .github/snapshots/slackreport.nf.test.snap | 1 - .github/snapshots/vscode.nf.test.snap | 1 - 23 files changed, 23 deletions(-) diff --git a/.github/snapshots/adaptivecard.nf.test.snap b/.github/snapshots/adaptivecard.nf.test.snap index fd0f6fd295..ba68358e9e 100644 --- a/.github/snapshots/adaptivecard.nf.test.snap +++ b/.github/snapshots/adaptivecard.nf.test.snap @@ -1,7 +1,6 @@ { "-profile test": { "content": [ - 4, { "FASTQC": { "fastqc": "0.12.1" diff --git a/.github/snapshots/changelog.nf.test.snap b/.github/snapshots/changelog.nf.test.snap index 3989533f59..cbeb2f9c6a 100644 --- a/.github/snapshots/changelog.nf.test.snap +++ b/.github/snapshots/changelog.nf.test.snap @@ -1,7 +1,6 @@ { "-profile test": { "content": [ - 4, { "FASTQC": { "fastqc": "0.12.1" diff --git a/.github/snapshots/ci.nf.test.snap b/.github/snapshots/ci.nf.test.snap index 39f8719f76..9435815267 100644 --- a/.github/snapshots/ci.nf.test.snap +++ b/.github/snapshots/ci.nf.test.snap @@ -1,7 +1,6 @@ { "-profile test": { "content": [ - 4, { "FASTQC": { "fastqc": "0.12.1" diff --git a/.github/snapshots/citations.nf.test.snap b/.github/snapshots/citations.nf.test.snap index 292367b69f..7ca53b2fd6 100644 --- a/.github/snapshots/citations.nf.test.snap +++ b/.github/snapshots/citations.nf.test.snap @@ -1,7 +1,6 @@ { "-profile test": { "content": [ - 4, { "FASTQC": { "fastqc": "0.12.1" diff --git a/.github/snapshots/code_linters.nf.test.snap b/.github/snapshots/code_linters.nf.test.snap index 292367b69f..7ca53b2fd6 100644 --- a/.github/snapshots/code_linters.nf.test.snap +++ b/.github/snapshots/code_linters.nf.test.snap @@ -1,7 +1,6 @@ { "-profile test": { "content": [ - 4, { "FASTQC": { "fastqc": "0.12.1" diff --git a/.github/snapshots/codespaces.nf.test.snap b/.github/snapshots/codespaces.nf.test.snap index 292367b69f..7ca53b2fd6 100644 --- a/.github/snapshots/codespaces.nf.test.snap +++ b/.github/snapshots/codespaces.nf.test.snap @@ -1,7 +1,6 @@ { "-profile test": { "content": [ - 4, { "FASTQC": { "fastqc": "0.12.1" diff --git a/.github/snapshots/default.nf.test.snap b/.github/snapshots/default.nf.test.snap index 31ea202d6a..0d1a057536 100644 --- a/.github/snapshots/default.nf.test.snap +++ b/.github/snapshots/default.nf.test.snap @@ -1,7 +1,6 @@ { "-profile test": { "content": [ - 4, { "FASTQC": { "fastqc": "0.12.1" diff --git a/.github/snapshots/documentation.nf.test.snap b/.github/snapshots/documentation.nf.test.snap index fd0f6fd295..ba68358e9e 100644 --- a/.github/snapshots/documentation.nf.test.snap +++ b/.github/snapshots/documentation.nf.test.snap @@ -1,7 +1,6 @@ { "-profile test": { "content": [ - 4, { "FASTQC": { "fastqc": "0.12.1" diff --git a/.github/snapshots/email.nf.test.snap b/.github/snapshots/email.nf.test.snap index fd0f6fd295..ba68358e9e 100644 --- a/.github/snapshots/email.nf.test.snap +++ b/.github/snapshots/email.nf.test.snap @@ -1,7 +1,6 @@ { "-profile test": { "content": [ - 4, { "FASTQC": { "fastqc": "0.12.1" diff --git a/.github/snapshots/fastqc.nf.test.snap b/.github/snapshots/fastqc.nf.test.snap index 66184b7b84..487fc5cdb7 100644 --- a/.github/snapshots/fastqc.nf.test.snap +++ b/.github/snapshots/fastqc.nf.test.snap @@ -1,7 +1,6 @@ { "-profile test": { "content": [ - 1, { "Workflow": { "my-prefix/testpipeline": "v1.0.0dev" diff --git a/.github/snapshots/github_badges.nf.test.snap b/.github/snapshots/github_badges.nf.test.snap index e671050699..c79757c35f 100644 --- a/.github/snapshots/github_badges.nf.test.snap +++ b/.github/snapshots/github_badges.nf.test.snap @@ -1,7 +1,6 @@ { "-profile test": { "content": [ - 4, { "FASTQC": { "fastqc": "0.12.1" diff --git a/.github/snapshots/gitpod.nf.test.snap b/.github/snapshots/gitpod.nf.test.snap index 292367b69f..7ca53b2fd6 100644 --- a/.github/snapshots/gitpod.nf.test.snap +++ b/.github/snapshots/gitpod.nf.test.snap @@ -1,7 +1,6 @@ { "-profile test": { "content": [ - 4, { "FASTQC": { "fastqc": "0.12.1" diff --git a/.github/snapshots/gpu.nf.test.snap b/.github/snapshots/gpu.nf.test.snap index eb83194a65..cffc9ac314 100644 --- a/.github/snapshots/gpu.nf.test.snap +++ b/.github/snapshots/gpu.nf.test.snap @@ -1,7 +1,6 @@ { "-profile test": { "content": [ - 4, { "FASTQC": { "fastqc": "0.12.1" diff --git a/.github/snapshots/igenomes.nf.test.snap b/.github/snapshots/igenomes.nf.test.snap index e7425c2b11..0855700461 100644 --- a/.github/snapshots/igenomes.nf.test.snap +++ b/.github/snapshots/igenomes.nf.test.snap @@ -1,7 +1,6 @@ { "-profile test": { "content": [ - 4, { "FASTQC": { "fastqc": "0.12.1" diff --git a/.github/snapshots/license.nf.test.snap b/.github/snapshots/license.nf.test.snap index fd0f6fd295..ba68358e9e 100644 --- a/.github/snapshots/license.nf.test.snap +++ b/.github/snapshots/license.nf.test.snap @@ -1,7 +1,6 @@ { "-profile test": { "content": [ - 4, { "FASTQC": { "fastqc": "0.12.1" diff --git a/.github/snapshots/modules.nf.test.snap b/.github/snapshots/modules.nf.test.snap index 05ff1ff447..0823cc7412 100644 --- a/.github/snapshots/modules.nf.test.snap +++ b/.github/snapshots/modules.nf.test.snap @@ -1,7 +1,6 @@ { "-profile test": { "content": [ - 0, null, [ "pipeline_info" diff --git a/.github/snapshots/multiqc.nf.test.snap b/.github/snapshots/multiqc.nf.test.snap index 542c7c30d2..12ea2b4e31 100644 --- a/.github/snapshots/multiqc.nf.test.snap +++ b/.github/snapshots/multiqc.nf.test.snap @@ -1,7 +1,6 @@ { "-profile test": { "content": [ - 3, null, [ "fastqc", diff --git a/.github/snapshots/nf_core_configs.nf.test.snap b/.github/snapshots/nf_core_configs.nf.test.snap index 292367b69f..7ca53b2fd6 100644 --- a/.github/snapshots/nf_core_configs.nf.test.snap +++ b/.github/snapshots/nf_core_configs.nf.test.snap @@ -1,7 +1,6 @@ { "-profile test": { "content": [ - 4, { "FASTQC": { "fastqc": "0.12.1" diff --git a/.github/snapshots/nf_schema.nf.test.snap b/.github/snapshots/nf_schema.nf.test.snap index f0703db991..402ddbc403 100644 --- a/.github/snapshots/nf_schema.nf.test.snap +++ b/.github/snapshots/nf_schema.nf.test.snap @@ -1,7 +1,6 @@ { "-profile test": { "content": [ - 4, { "FASTQC": { "fastqc": "0.12.1" diff --git a/.github/snapshots/rocrate.nf.test.snap b/.github/snapshots/rocrate.nf.test.snap index fd0f6fd295..ba68358e9e 100644 --- a/.github/snapshots/rocrate.nf.test.snap +++ b/.github/snapshots/rocrate.nf.test.snap @@ -1,7 +1,6 @@ { "-profile test": { "content": [ - 4, { "FASTQC": { "fastqc": "0.12.1" diff --git a/.github/snapshots/seqera_platform.nf.test.snap b/.github/snapshots/seqera_platform.nf.test.snap index fd0f6fd295..ba68358e9e 100644 --- a/.github/snapshots/seqera_platform.nf.test.snap +++ b/.github/snapshots/seqera_platform.nf.test.snap @@ -1,7 +1,6 @@ { "-profile test": { "content": [ - 4, { "FASTQC": { "fastqc": "0.12.1" diff --git a/.github/snapshots/slackreport.nf.test.snap b/.github/snapshots/slackreport.nf.test.snap index fd0f6fd295..ba68358e9e 100644 --- a/.github/snapshots/slackreport.nf.test.snap +++ b/.github/snapshots/slackreport.nf.test.snap @@ -1,7 +1,6 @@ { "-profile test": { "content": [ - 4, { "FASTQC": { "fastqc": "0.12.1" diff --git a/.github/snapshots/vscode.nf.test.snap b/.github/snapshots/vscode.nf.test.snap index fd0f6fd295..ba68358e9e 100644 --- a/.github/snapshots/vscode.nf.test.snap +++ b/.github/snapshots/vscode.nf.test.snap @@ -1,7 +1,6 @@ { "-profile test": { "content": [ - 4, { "FASTQC": { "fastqc": "0.12.1"