diff --git a/.nf-core.yml b/.nf-core.yml index d06a384d..761a0c85 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -9,11 +9,11 @@ lint: nf_core_version: 3.3.2 repository_type: pipeline template: - author: Bailey PJ, Botvinnik O, Marques de Almeida F, Peltzer A, Sturm G + author: Bailey PJ, Botvinnik O, Marques de Almeida F, Peltzer A, Sturm G, Dongze H description: Pipeline for processing 10x Genomics single cell rnaseq data force: false is_nfcore: true name: scrnaseq org: nf-core outdir: . - version: 2.8.0dev + version: 4.1.0 diff --git a/CHANGELOG.md b/CHANGELOG.md index 28b86195..d181a907 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,20 +3,31 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). -## v4.1.0dev +## v4.1.0 - 2025-08-01 + +### Features -- Update nextflow_schema.json - Fix simpleaf protocol name for 10xv4 ([#452](https://github.com/nf-core/scrnaseq/pull/452)) - Fix the workflow for cellranger-arc alignment and add new test with 10x multiome dataset ([#441](https://github.com/nf-core/scrnaseq/pull/441)) -- Update `nf-core/cellranger` modules to tool verson `9.0.1` ([#467](https://github.com/nf-core/scrnaseq/pull/467)). -- Fix igenomes usage to correctly handle fasta and gtf files ([#469](https://github.com/nf-core/scrnaseq/pull/469)). -- Update `cellranger/multi` module to latest version with nf-core tools ([#482](https://github.com/nf-core/scrnaseq/pull/482)). -- Adapt pipeline to also parse `OCM` barcodes for `cellranger/multi` and update its documentation ([#482](https://github.com/nf-core/scrnaseq/pull/482)). -- Fix that skip_multiqc parameter did not work ([#479](https://github.com/nf-core/scrnaseq/pull/479)). +- Update `nf-core/cellranger` modules to tool version `9.0.1` ([#467](https://github.com/nf-core/scrnaseq/pull/467)) +- Fix igenomes usage to correctly handle fasta and gtf files ([#469](https://github.com/nf-core/scrnaseq/pull/469)) +- Update `cellranger/multi` module to latest version with nf-core tools ([#482](https://github.com/nf-core/scrnaseq/pull/482)) +- Adapt pipeline to also parse `OCM` barcodes for `cellranger/multi` and update its documentation ([#482](https://github.com/nf-core/scrnaseq/pull/482)) +- Fix that skip_multiqc parameter did not work ([#479](https://github.com/nf-core/scrnaseq/pull/479)) +- Add the `accelerator` process directive to the `process_gpu` label ([#477](https://github.com/nf-core/scrnaseq/pull/477)) +- Refactor iGenomes handling to expose params object pipeline-wide ([#483](https://github.com/nf-core/scrnaseq/pull/483)) + +### Documentation + +- Update nextflow_schema.json ([#453](https://github.com/nf-core/scrnaseq/pull/453)) +- Update `--cellranger_index` docs to point out that the base index directory is needed ([#458](https://github.com/nf-core/scrnaseq/pull/458)) +- Update protocol documentation ([#459](https://github.com/nf-core/scrnaseq/pull/459)) ### Chore - Add ruff pre-commit check as linter/autoformatter for python scripts ([#464](https://github.com/nf-core/scrnaseq/pull/464)) +- Template update for nf-core/tools v3.2.1 ([#466](https://github.com/nf-core/scrnaseq/pull/466)) +- Template update for nf-core/tools v3.3.2 ([#474](https://github.com/nf-core/scrnaseq/pull/474)) ## v4.0.0 - 2025-03-10 diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index c7623303..708b4c67 100644 --- a/assets/multiqc_config.yml +++ b/assets/multiqc_config.yml @@ -1,7 +1,7 @@ report_comment: > - This report has been generated by the nf-core/scrnaseq analysis pipeline. For information about how - to interpret these results, please see the documentation. report_section_order: "nf-core-scrnaseq-methods-description": diff --git a/nextflow.config b/nextflow.config index db12ed0c..91ce264c 100644 --- a/nextflow.config +++ b/nextflow.config @@ -343,7 +343,7 @@ manifest { mainScript = 'main.nf' defaultBranch = 'master' nextflowVersion = '!>=24.10.5' - version = '4.1.0dev' + version = '4.1.0' doi = '10.5281/zenodo.3568187' } diff --git a/nf-test.config b/nf-test.config index 3a1fff59..b3f60e80 100644 --- a/nf-test.config +++ b/nf-test.config @@ -19,6 +19,6 @@ config { // load the necessary plugins plugins { - load "nft-utils@0.0.3" + load "nft-utils@0.0.5" } } diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json index 149c69ed..cc836b47 100644 --- a/ro-crate-metadata.json +++ b/ro-crate-metadata.json @@ -21,8 +21,8 @@ { "@id": "./", "@type": "Dataset", - "creativeWorkStatus": "InProgress", - "datePublished": "2025-07-08T11:39:16+00:00", + "creativeWorkStatus": "Stable", + "datePublished": "2025-08-01T12:39:51+00:00", "description": "

\n \n \n \"nf-core/scrnaseq\"\n \n

\n\n[![GitHub Actions CI Status](https://github.com/nf-core/scrnaseq/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/scrnaseq/actions/workflows/nf-test.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/scrnaseq/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/scrnaseq/actions/workflows/linting.yml)\n[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/scrnaseq/results)\n[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.3568187-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.3568187)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n\n[![Nextflow](https://img.shields.io/badge/version-%E2%89%A524.10.5-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)\n[![nf-core template version](https://img.shields.io/badge/nf--core_template-3.3.2-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.3.2)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/scrnaseq)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23scrnaseq-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/scrnaseq)[![Follow on Bluesky](https://img.shields.io/badge/bluesky-%40nf__core-1185fe?labelColor=000000&logo=bluesky)](https://bsky.app/profile/nf-co.re)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)\n\n## Introduction\n\n**nf-core/scrnaseq** is a bioinformatics best-practice analysis pipeline for processing 10x Genomics single-cell RNA-seq data.\n\nThis is a community effort in building a pipeline capable to support:\n\n- SimpleAF(Alevin-Fry) + AlevinQC\n- STARSolo\n- Kallisto + BUStools\n- Cellranger\n\n> [!IMPORTANT]\n> Cellranger is a commercial tool from 10X Genomics Inc. and falls under the EULA from 10X Genomics Inc. The container provided for the CellRanger functionality in this pipeline has been built by the nf-core community and is therefore _not supported by 10X genomics_ directly. We are in discussions with 10X on how to improve the user experience and licence situation for both us as a community as well as 10X and end users and will update this statement here accordingly.\n\n## Documentation\n\nThe nf-core/scrnaseq pipeline comes with documentation about the pipeline [usage](https://nf-co.re/scrnaseq/usage), [parameters](https://nf-co.re/scrnaseq/parameters) and [output](https://nf-co.re/scrnaseq/output).\n\n![scrnaseq workflow](docs/images/scrnaseq_pipeline_V3.0-metro_clean.png)\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.\n\nFirst, prepare a samplesheet with your input data that looks as follows:\n\n`samplesheet.csv`:\n\n```csv\nsample,fastq_1,fastq_2,expected_cells\npbmc8k,pbmc8k_S1_L007_R1_001.fastq.gz,pbmc8k_S1_L007_R2_001.fastq.gz,10000\npbmc8k,pbmc8k_S1_L008_R1_001.fastq.gz,pbmc8k_S1_L008_R2_001.fastq.gz,10000\n```\n\nEach row represents a fastq file (single-end) or a pair of fastq files (paired end).\n\nNow, you can run the pipeline using:\n\n```bash\nnextflow run nf-core/scrnaseq \\\n -profile \\\n --input samplesheet.csv \\\n --fasta GRCm38.p6.genome.chr19.fa \\\n --gtf gencode.vM19.annotation.chr19.gtf \\\n --protocol 10XV2 \\\n --aligner \\\n --outdir \n```\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/scrnaseq/usage) and the [parameter documentation](https://nf-co.re/scrnaseq/parameters).\n\n## Decision Tree for users\n\nThe nf-core/scrnaseq pipeline features several paths to analyze your single cell data. Future additions will also be done soon, e.g. the addition of multi-ome analysis types. To aid users in analyzing their data, we have added a decision tree to help people decide on what type of analysis they want to run and how to choose appropriate parameters for that.\n\n```mermaid\ngraph TD\n A[sc RNA] -->|alevin-fry| B(h5ad/seurat/mtx matrices)\n A[sc RNA] -->|CellRanger| B(h5ad/seurat/mtx matrices)\n A[sc RNA] -->|kbpython| B(h5ad/seurat/mtx matrices)\n A[sc RNA] -->|STARsolo| B(h5ad/seurat/mtx matrices)\n```\n\nOptions for the respective alignment method can be found [here](https://nf-co.re/scrnaseq/docs/usage/#aligning-options) to choose between methods.\n\n## Pipeline output\n\nTo see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/scrnaseq/results) tab on the nf-core website pipeline page.\nFor more details about the output files and reports, please refer to the\n[output documentation](https://nf-co.re/scrnaseq/output).\n\n## Credits\n\nnf-core/scrnaseq was originally written by Bailey PJ, Botvinnik O, Marques de Almeida F, Gabernet G, Peltzer A, Sturm G.\n\nWe thank the following people and teams for their extensive assistance in the development of this pipeline:\n\n- @heylf\n- @KevinMenden\n- @FloWuenne\n- @rob-p\n- [GHGA](https://www.ghga.de/)\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#scrnaseq` channel](https://nfcore.slack.com/channels/scrnaseq) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\nIf you use nf-core/scrnaseq for your analysis, please cite it using the following doi: [10.5281/zenodo.3568187](https://doi.org/10.5281/zenodo.3568187)\n\nThe basic benchmarks that were used as motivation for incorporating the available modular workflows can be found in [this publication](https://www.biorxiv.org/content/10.1101/673285v2).\n\nWe offer all three paths for the processing of scRNAseq data so it remains up to the user to decide which pipeline workflow is chosen for a particular analysis question.\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n", "hasPart": [ { @@ -108,7 +108,7 @@ }, "mentions": [ { - "@id": "#244931f2-1b9e-455a-a8b4-139a382be3a1" + "@id": "#d42b5d10-79f6-4e28-83e9-a0b50343b820" } ], "name": "nf-core/scrnaseq" @@ -137,19 +137,22 @@ ], "creator": [ { - "@id": "https://orcid.org/0000-0001-5010-9539" + "@id": "https://orcid.org/0000-0001-9584-7842" }, { - "@id": "https://orcid.org/0000-0003-4412-7970" + "@id": "https://orcid.org/0000-0002-6503-2180" }, { - "@id": "https://orcid.org/0000-0002-6503-2180" + "@id": "https://orcid.org/0000-0002-2705-1727" + }, + { + "@id": "#rob.syme@gmail.com" }, { "@id": "https://orcid.org/0000-0002-4639-0935" }, { - "@id": "https://orcid.org/0000-0001-9584-7842" + "@id": "https://orcid.org/0000-0001-5010-9539" }, { "@id": "#drpatelhh@gmail.com" @@ -158,11 +161,11 @@ "@id": "#felipemarques89@gmail.com" }, { - "@id": "#rob.syme@gmail.com" + "@id": "https://orcid.org/0000-0003-4412-7970" } ], "dateCreated": "", - "dateModified": "2025-07-08T11:39:16Z", + "dateModified": "2025-08-01T12:39:51Z", "dct:conformsTo": "https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE/", "keywords": [ "nf-core", @@ -191,10 +194,10 @@ }, "url": [ "https://github.com/nf-core/scrnaseq", - "https://nf-co.re/scrnaseq/dev/" + "https://nf-co.re/scrnaseq/4.1.0/" ], "version": [ - "4.1.0dev" + "4.1.0" ] }, { @@ -210,11 +213,11 @@ "version": "!>=24.10.5" }, { - "@id": "#244931f2-1b9e-455a-a8b4-139a382be3a1", + "@id": "#d42b5d10-79f6-4e28-83e9-a0b50343b820", "@type": "TestSuite", "instance": [ { - "@id": "#72edb790-585a-4a53-862b-83177c420bf1" + "@id": "#33a6fef4-8636-4fc4-9035-63bea60f3fb6" } ], "mainEntity": { @@ -223,7 +226,7 @@ "name": "Test suite for nf-core/scrnaseq" }, { - "@id": "#72edb790-585a-4a53-862b-83177c420bf1", + "@id": "#33a6fef4-8636-4fc4-9035-63bea60f3fb6", "@type": "TestInstance", "name": "GitHub Actions workflow for testing nf-core/scrnaseq", "resource": "repos/nf-core/scrnaseq/actions/workflows/nf-test.yml", @@ -367,16 +370,10 @@ "url": "https://nf-co.re/" }, { - "@id": "https://orcid.org/0000-0001-5010-9539", - "@type": "Person", - "email": "sangramsahu15@gmail.com", - "name": "Sangram Keshari Sahu" - }, - { - "@id": "https://orcid.org/0000-0003-4412-7970", + "@id": "https://orcid.org/0000-0001-9584-7842", "@type": "Person", - "email": "olga.botvinnik@gmail.com", - "name": "Olga Botvinnik" + "email": "mail@gregor-sturm.de", + "name": "Gregor Sturm" }, { "@id": "https://orcid.org/0000-0002-6503-2180", @@ -384,6 +381,18 @@ "email": "apeltzer@users.noreply.github.com", "name": "Alexander Peltzer" }, + { + "@id": "https://orcid.org/0000-0002-2705-1727", + "@type": "Person", + "email": "60394289+LeonHafner@users.noreply.github.com", + "name": "Leon Hafner" + }, + { + "@id": "#rob.syme@gmail.com", + "@type": "Person", + "email": "rob.syme@gmail.com", + "name": "Rob Syme" + }, { "@id": "https://orcid.org/0000-0002-4639-0935", "@type": "Person", @@ -391,10 +400,10 @@ "name": "Nico Trummer" }, { - "@id": "https://orcid.org/0000-0001-9584-7842", + "@id": "https://orcid.org/0000-0001-5010-9539", "@type": "Person", - "email": "mail@gregor-sturm.de", - "name": "Gregor Sturm" + "email": "sangramsahu15@gmail.com", + "name": "Sangram Keshari Sahu" }, { "@id": "#drpatelhh@gmail.com", @@ -409,10 +418,10 @@ "name": "Felipe Marques de Almeida" }, { - "@id": "#rob.syme@gmail.com", + "@id": "https://orcid.org/0000-0003-4412-7970", "@type": "Person", - "email": "rob.syme@gmail.com", - "name": "Rob Syme" + "email": "olga.botvinnik@gmail.com", + "name": "Olga Botvinnik" } ] } \ No newline at end of file diff --git a/tests/main_pipeline_cellranger.nf.test b/tests/main_pipeline_cellranger.nf.test index ca27b24f..4ee158b9 100644 --- a/tests/main_pipeline_cellranger.nf.test +++ b/tests/main_pipeline_cellranger.nf.test @@ -24,7 +24,7 @@ nextflow_pipeline { // 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("$params.outdir/pipeline_info/nf_core_scrnaseq_software_mqc_versions.yml"), + removeFromYamlMap("$params.outdir/pipeline_info/nf_core_scrnaseq_software_mqc_versions.yml", "Workflow"), // All stable path name, with a relative path stable_name, // All files with stable contents diff --git a/tests/main_pipeline_cellranger.nf.test.snap b/tests/main_pipeline_cellranger.nf.test.snap index ebdd1d45..3d1813ac 100644 --- a/tests/main_pipeline_cellranger.nf.test.snap +++ b/tests/main_pipeline_cellranger.nf.test.snap @@ -16,13 +16,10 @@ "fastqc": "0.12.1" }, "MTX_TO_H5AD": { - "python": "3.12.5", - "scanpy": "1.10.2", + "anndata": "0.10.8", "pandas": "2.2.2", - "anndata": "0.10.8" - }, - "Workflow": { - "nf-core/scrnaseq": "v4.1.0dev" + "python": "3.12.5", + "scanpy": "1.10.2" } }, [ @@ -383,8 +380,8 @@ ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.1" + "nextflow": "25.04.6" }, - "timestamp": "2025-08-01T11:05:37.982319489" + "timestamp": "2025-08-04T08:28:33.037302748" } } \ No newline at end of file diff --git a/tests/main_pipeline_cellrangerarc.nf.test b/tests/main_pipeline_cellrangerarc.nf.test index eb23a6f8..49ec6b57 100644 --- a/tests/main_pipeline_cellrangerarc.nf.test +++ b/tests/main_pipeline_cellrangerarc.nf.test @@ -29,7 +29,7 @@ nextflow_pipeline { // 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("$params.outdir/pipeline_info/nf_core_scrnaseq_software_mqc_versions.yml"), + removeFromYamlMap("$params.outdir/pipeline_info/nf_core_scrnaseq_software_mqc_versions.yml", "Workflow"), // All stable path name, with a relative path stable_name, // All files with stable contents diff --git a/tests/main_pipeline_cellrangerarc.nf.test.snap b/tests/main_pipeline_cellrangerarc.nf.test.snap index 296e766c..c0994daf 100644 --- a/tests/main_pipeline_cellrangerarc.nf.test.snap +++ b/tests/main_pipeline_cellrangerarc.nf.test.snap @@ -16,13 +16,10 @@ "fastqc": "0.12.1" }, "MTX_TO_H5AD": { - "python": "3.12.5", - "scanpy": "1.10.2", + "anndata": "0.10.8", "pandas": "2.2.2", - "anndata": "0.10.8" - }, - "Workflow": { - "nf-core/scrnaseq": "v4.1.0dev" + "python": "3.12.5", + "scanpy": "1.10.2" } }, [ @@ -286,8 +283,8 @@ ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.1" + "nextflow": "25.04.6" }, - "timestamp": "2025-08-01T11:18:19.395555812" + "timestamp": "2025-08-04T08:33:34.787444894" } } \ No newline at end of file diff --git a/tests/main_pipeline_cellrangermulti.nf.test b/tests/main_pipeline_cellrangermulti.nf.test index 475975b3..2d6e6a4a 100644 --- a/tests/main_pipeline_cellrangermulti.nf.test +++ b/tests/main_pipeline_cellrangermulti.nf.test @@ -35,7 +35,7 @@ nextflow_pipeline { // 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("$params.outdir/pipeline_info/nf_core_scrnaseq_software_mqc_versions.yml"), + removeFromYamlMap("$params.outdir/pipeline_info/nf_core_scrnaseq_software_mqc_versions.yml", "Workflow"), // All stable path name, with a relative path stable_name, // All files with stable contents @@ -73,7 +73,7 @@ nextflow_pipeline { // 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("$params.outdir/pipeline_info/nf_core_scrnaseq_software_mqc_versions.yml"), + removeFromYamlMap("$params.outdir/pipeline_info/nf_core_scrnaseq_software_mqc_versions.yml", "Workflow"), // All stable path name, with a relative path stable_name, // All files with stable contents diff --git a/tests/main_pipeline_cellrangermulti.nf.test.snap b/tests/main_pipeline_cellrangermulti.nf.test.snap index a226e533..d1154bf4 100644 --- a/tests/main_pipeline_cellrangermulti.nf.test.snap +++ b/tests/main_pipeline_cellrangermulti.nf.test.snap @@ -25,13 +25,10 @@ "gunzip": 1.1 }, "MTX_TO_H5AD": { - "python": "3.12.5", - "scanpy": "1.10.2", + "anndata": "0.10.8", "pandas": "2.2.2", - "anndata": "0.10.8" - }, - "Workflow": { - "nf-core/scrnaseq": "v4.1.0dev" + "python": "3.12.5", + "scanpy": "1.10.2" } }, [ @@ -1247,9 +1244,9 @@ ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.1" + "nextflow": "25.04.6" }, - "timestamp": "2025-08-01T11:43:41.46111504" + "timestamp": "2025-08-04T08:47:14.585663687" }, "test-dataset_cellrangermulti_aligner_rat": { "content": [ @@ -1277,13 +1274,10 @@ "gunzip": 1.1 }, "MTX_TO_H5AD": { - "python": "3.12.5", - "scanpy": "1.10.2", + "anndata": "0.10.8", "pandas": "2.2.2", - "anndata": "0.10.8" - }, - "Workflow": { - "nf-core/scrnaseq": "v4.1.0dev" + "python": "3.12.5", + "scanpy": "1.10.2" } }, [ @@ -1854,8 +1848,8 @@ ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.1" + "nextflow": "25.04.6" }, - "timestamp": "2025-08-01T12:02:57.754836314" + "timestamp": "2025-08-04T08:56:26.746631285" } } \ No newline at end of file diff --git a/tests/main_pipeline_kallisto.nf.test b/tests/main_pipeline_kallisto.nf.test index ed1cef27..bc74dbac 100644 --- a/tests/main_pipeline_kallisto.nf.test +++ b/tests/main_pipeline_kallisto.nf.test @@ -24,7 +24,7 @@ nextflow_pipeline { // 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("$params.outdir/pipeline_info/nf_core_scrnaseq_software_mqc_versions.yml"), + removeFromYamlMap("$params.outdir/pipeline_info/nf_core_scrnaseq_software_mqc_versions.yml", "Workflow"), // All stable path name, with a relative path stable_name, // All files with stable contents diff --git a/tests/main_pipeline_kallisto.nf.test.snap b/tests/main_pipeline_kallisto.nf.test.snap index 331163ba..c2eb8ebd 100644 --- a/tests/main_pipeline_kallisto.nf.test.snap +++ b/tests/main_pipeline_kallisto.nf.test.snap @@ -13,13 +13,10 @@ "kallistobustools": "0.28.2" }, "MTX_TO_H5AD": { - "python": "3.12.5", - "scanpy": "1.10.2", + "anndata": "0.10.8", "pandas": "2.2.2", - "anndata": "0.10.8" - }, - "Workflow": { - "nf-core/scrnaseq": "v4.1.0dev" + "python": "3.12.5", + "scanpy": "1.10.2" } }, [ @@ -212,8 +209,8 @@ ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.1" + "nextflow": "25.04.6" }, - "timestamp": "2025-08-01T12:08:34.446984853" + "timestamp": "2025-08-04T09:00:22.183689983" } } \ No newline at end of file diff --git a/tests/main_pipeline_simpleaf.nf.test b/tests/main_pipeline_simpleaf.nf.test index 4e4bfd36..19972fa2 100644 --- a/tests/main_pipeline_simpleaf.nf.test +++ b/tests/main_pipeline_simpleaf.nf.test @@ -24,7 +24,7 @@ nextflow_pipeline { // 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("$params.outdir/pipeline_info/nf_core_scrnaseq_software_mqc_versions.yml"), + removeFromYamlMap("$params.outdir/pipeline_info/nf_core_scrnaseq_software_mqc_versions.yml", "Workflow"), // All stable path name, with a relative path stable_name, // All files with stable contents diff --git a/tests/main_pipeline_simpleaf.nf.test.snap b/tests/main_pipeline_simpleaf.nf.test.snap index 03ebe617..eb4e9549 100644 --- a/tests/main_pipeline_simpleaf.nf.test.snap +++ b/tests/main_pipeline_simpleaf.nf.test.snap @@ -10,10 +10,10 @@ "fastqc": "0.12.1" }, "MTX_TO_H5AD": { - "python": "3.12.5", - "scanpy": "1.10.2", + "anndata": "0.10.8", "pandas": "2.2.2", - "anndata": "0.10.8" + "python": "3.12.5", + "scanpy": "1.10.2" }, "SIMPLEAF_INDEX": { "alevin-fry": "0.11.2", @@ -26,9 +26,6 @@ "piscem": "0.12.2", "salmon": "1.10.3", "simpleaf": "0.19.4" - }, - "Workflow": { - "nf-core/scrnaseq": "v4.1.0dev" } }, [ @@ -186,8 +183,8 @@ ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.1" + "nextflow": "25.04.6" }, - "timestamp": "2025-08-01T12:17:17.575430596" + "timestamp": "2025-08-04T09:02:37.806014973" } } \ No newline at end of file diff --git a/tests/main_pipeline_star.nf.test b/tests/main_pipeline_star.nf.test index 288a95cb..81f52cc6 100644 --- a/tests/main_pipeline_star.nf.test +++ b/tests/main_pipeline_star.nf.test @@ -24,7 +24,7 @@ nextflow_pipeline { // 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("$params.outdir/pipeline_info/nf_core_scrnaseq_software_mqc_versions.yml"), + removeFromYamlMap("$params.outdir/pipeline_info/nf_core_scrnaseq_software_mqc_versions.yml", "Workflow"), // All stable path name, with a relative path stable_name, // All files with stable contents diff --git a/tests/main_pipeline_star.nf.test.snap b/tests/main_pipeline_star.nf.test.snap index 47d0551b..11204653 100644 --- a/tests/main_pipeline_star.nf.test.snap +++ b/tests/main_pipeline_star.nf.test.snap @@ -7,21 +7,18 @@ "fastqc": "0.12.1" }, "MTX_TO_H5AD": { - "python": "3.12.5", - "scanpy": "1.10.2", + "anndata": "0.10.8", "pandas": "2.2.2", - "anndata": "0.10.8" + "python": "3.12.5", + "scanpy": "1.10.2" }, "STAR_ALIGN": { "star": "2.7.10b" }, "STAR_GENOMEGENERATE": { - "star": "2.7.10a", + "gawk": "5.1.0", "samtools": 1.18, - "gawk": "5.1.0" - }, - "Workflow": { - "nf-core/scrnaseq": "v4.1.0dev" + "star": "2.7.10a" } }, [ @@ -233,8 +230,8 @@ ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.1" + "nextflow": "25.04.6" }, - "timestamp": "2025-08-01T12:28:41.241504112" + "timestamp": "2025-08-04T09:08:55.70547428" } } \ No newline at end of file