From 5327c139dfae7cbdc3e66eae4adbd390d3a260f2 Mon Sep 17 00:00:00 2001 From: Matthieu Muffato Date: Fri, 28 Mar 2025 13:11:38 +0000 Subject: [PATCH 1/5] Fixed the changelog --- CHANGELOG.md | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 0e3fa8ab..3734fda7 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,7 +3,9 @@ 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). -## [[0.7.1](https://github.com/sanger-tol/blobtoolkit/releases/tag/0.7.1)] – Psyduck (patch 1) – [2025-03-297 +## [[0.7.1](https://github.com/sanger-tol/blobtoolkit/releases/tag/0.7.1)] – Psyduck (patch 1) – [2025-03-29] + +### Enhancements & fixes - Upgraded the blobtools version which contains a bugfix @@ -17,6 +19,8 @@ Note, since the pipeline is using Nextflow DSL2, each process will be run with i ## [[0.7.0](https://github.com/sanger-tol/blobtoolkit/releases/tag/0.7.0)] – Psyduck – [2025-03-19] +### Enhancements & fixes + - Fetch information about the chromosomes of the assemblies. Used to power "grid plots". - Fill in accurate read information in the blobDir. Users are now reqiured @@ -54,6 +58,8 @@ Note, since the pipeline is using Nextflow DSL2, each process will be run with i ## [[0.6.0](https://github.com/sanger-tol/blobtoolkit/releases/tag/0.6.0)] – Bellsprout – [2024-09-13] +### Enhancements & fixes + The pipeline has now been validated for draft (unpublished) assemblies. - The pipeline now queries the NCBI database instead of GoaT to establish the From b635d60452d6e19e21d0726ec15422d55fcfdbe8 Mon Sep 17 00:00:00 2001 From: sanger-tolsoft <105875386+sanger-tolsoft@users.noreply.github.com> Date: Thu, 3 Apr 2025 19:22:02 +0000 Subject: [PATCH 2/5] Template update for nf-core/tools version 3.2.0 --- .nf-core.yml | 56 +++++++++++++++++++-------------------- CHANGELOG.md | 2 +- assets/multiqc_config.yml | 2 +- nextflow.config | 2 +- ro-crate-metadata.json | 32 +++++++++++----------- 5 files changed, 47 insertions(+), 47 deletions(-) diff --git a/.nf-core.yml b/.nf-core.yml index 2a4ce6d7..05668f74 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -1,35 +1,35 @@ lint: files_exist: - - CODE_OF_CONDUCT.md - - assets/nf-core-blobtoolkit_logo_light.png - - docs/images/nf-core-blobtoolkit_logo_light.png - - docs/images/nf-core-blobtoolkit_logo_dark.png - - .github/ISSUE_TEMPLATE/config.yml - - .github/workflows/awstest.yml - - .github/workflows/awsfulltest.yml - - conf/igenomes.config + - CODE_OF_CONDUCT.md + - assets/nf-core-blobtoolkit_logo_light.png + - docs/images/nf-core-blobtoolkit_logo_light.png + - docs/images/nf-core-blobtoolkit_logo_dark.png + - .github/ISSUE_TEMPLATE/config.yml + - .github/workflows/awstest.yml + - .github/workflows/awsfulltest.yml + - conf/igenomes.config files_unchanged: - - LICENCE - - lib/NfcoreTemplate.groovy - - CODE_OF_CONDUCT.md - - assets/sendmail_template.txt - - assets/email_template.html - - assets/email_template.txt - - assets/nf-core-blobtoolkit_logo_light.png - - docs/images/nf-core-blobtoolkit_logo_light.png - - docs/images/nf-core-blobtoolkit_logo_dark.png - - .github/ISSUE_TEMPLATE/bug_report.yml - - .github/PULL_REQUEST_TEMPLATE.md - - .github/workflows/linting.yml - - .github/workflows/branch.yml - - .github/CONTRIBUTING.md - - .github/workflows/linting_comment.yml + - LICENCE + - lib/NfcoreTemplate.groovy + - CODE_OF_CONDUCT.md + - assets/sendmail_template.txt + - assets/email_template.html + - assets/email_template.txt + - assets/nf-core-blobtoolkit_logo_light.png + - docs/images/nf-core-blobtoolkit_logo_light.png + - docs/images/nf-core-blobtoolkit_logo_dark.png + - .github/ISSUE_TEMPLATE/bug_report.yml + - .github/PULL_REQUEST_TEMPLATE.md + - .github/workflows/linting.yml + - .github/workflows/branch.yml + - .github/CONTRIBUTING.md + - .github/workflows/linting_comment.yml merge_markers: false multiqc_config: - - report_comment + - report_comment nextflow_config: - - manifest.name - - manifest.homePage + - manifest.name + - manifest.homePage template_strings: false nf_core_version: 3.2.0 repository_type: pipeline @@ -42,5 +42,5 @@ template: org: sanger-tol outdir: . skip_features: - - igenomes - version: 0.7.0 + - igenomes + version: 0.7.1 diff --git a/CHANGELOG.md b/CHANGELOG.md index 06e20df2..14e7669f 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,7 +3,7 @@ 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). -## v0.7.0 - [date] +## v0.7.1 - [date] Initial release of sanger-tol/blobtoolkit, created with the [nf-core](https://nf-co.re/) template. diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index d5c59938..0510c3d5 100644 --- a/assets/multiqc_config.yml +++ b/assets/multiqc_config.yml @@ -1,5 +1,5 @@ report_comment: > - This report has been generated by the sanger-tol/blobtoolkit + This report has been generated by the sanger-tol/blobtoolkit analysis pipeline. report_section_order: "sanger-tol-blobtoolkit-methods-description": diff --git a/nextflow.config b/nextflow.config index 9254da6f..7844139e 100644 --- a/nextflow.config +++ b/nextflow.config @@ -237,7 +237,7 @@ manifest { mainScript = 'main.nf' defaultBranch = 'main' nextflowVersion = '!>=24.04.2' - version = '0.7.0' + version = '0.7.1' doi = '' } diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json index dc61b0c4..db1d55b1 100644 --- a/ro-crate-metadata.json +++ b/ro-crate-metadata.json @@ -22,7 +22,7 @@ "@id": "./", "@type": "Dataset", "creativeWorkStatus": "Stable", - "datePublished": "2025-03-07T13:35:10+00:00", + "datePublished": "2025-04-03T19:22:00+00:00", "description": "# sanger-tol/blobtoolkit\n\n[![GitHub Actions CI Status](https://github.com/sanger-tol/blobtoolkit/actions/workflows/ci.yml/badge.svg)](https://github.com/sanger-tol/blobtoolkit/actions/workflows/ci.yml)\n[![GitHub Actions Linting Status](https://github.com/sanger-tol/blobtoolkit/actions/workflows/linting.yml/badge.svg)](https://github.com/sanger-tol/blobtoolkit/actions/workflows/linting.yml)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)\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/nextflow%20DSL2-%E2%89%A524.04.2-23aa62.svg)](https://www.nextflow.io/)\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/sanger-tol/blobtoolkit)\n\n## Introduction\n\n**sanger-tol/blobtoolkit** is a bioinformatics pipeline that ...\n\n\n\n\n1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))\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\n\n\nNow, you can run the pipeline using:\n\n\n\n```bash\nnextflow run sanger-tol/blobtoolkit \\\n -profile \\\n --input samplesheet.csv \\\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\n## Credits\n\nsanger-tol/blobtoolkit was originally written by priyanka-surana.\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).\n\n## Citations\n\n\n\n\n\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nThis pipeline uses code and infrastructure developed and maintained by the [nf-core](https://nf-co.re) community, reused here under the [MIT license](https://github.com/nf-core/tools/blob/main/LICENSE).\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n", "hasPart": [ { @@ -93,7 +93,7 @@ }, "mentions": [ { - "@id": "#8275489f-2726-4d94-b502-adfbd72b7b9d" + "@id": "#040370e7-e13b-4de6-9268-07dc566af218" } ], "name": "sanger-tol/blobtoolkit" @@ -122,14 +122,14 @@ ], "creator": [ { - "@id": "#ps22@sanger.ac.uk" + "@id": "https://orcid.org/0000-0002-7860-3560" }, { - "@id": "https://orcid.org/0000-0002-7860-3560" + "@id": "#ps22@sanger.ac.uk" } ], "dateCreated": "", - "dateModified": "2025-03-07T13:35:10Z", + "dateModified": "2025-04-03T19:22:00Z", "dct:conformsTo": "https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE/", "keywords": [ "nf-core", @@ -149,10 +149,10 @@ }, "url": [ "https://github.com/sanger-tol/blobtoolkit", - "https://nf-co.re/sanger-tol/blobtoolkit/0.7.0/" + "https://nf-co.re/sanger-tol/blobtoolkit/0.7.1/" ], "version": [ - "0.7.0" + "0.7.1" ] }, { @@ -168,11 +168,11 @@ "version": "!>=24.04.2" }, { - "@id": "#8275489f-2726-4d94-b502-adfbd72b7b9d", + "@id": "#040370e7-e13b-4de6-9268-07dc566af218", "@type": "TestSuite", "instance": [ { - "@id": "#c10b809d-8e67-421b-acff-2c4de88bcf1f" + "@id": "#1489a662-31a8-4c51-92a7-bada870a94dd" } ], "mainEntity": { @@ -181,7 +181,7 @@ "name": "Test suite for sanger-tol/blobtoolkit" }, { - "@id": "#c10b809d-8e67-421b-acff-2c4de88bcf1f", + "@id": "#1489a662-31a8-4c51-92a7-bada870a94dd", "@type": "TestInstance", "name": "GitHub Actions workflow for testing sanger-tol/blobtoolkit", "resource": "repos/sanger-tol/blobtoolkit/actions/workflows/ci.yml", @@ -299,17 +299,17 @@ "name": "nf-core", "url": "https://nf-co.re/" }, - { - "@id": "#ps22@sanger.ac.uk", - "@type": "Person", - "email": "ps22@sanger.ac.uk", - "name": "Priyanka Surana" - }, { "@id": "https://orcid.org/0000-0002-7860-3560", "@type": "Person", "email": "mm49@sanger.ac.uk", "name": "Matthieu Muffato" + }, + { + "@id": "#ps22@sanger.ac.uk", + "@type": "Person", + "email": "ps22@sanger.ac.uk", + "name": "Priyanka Surana" } ] } \ No newline at end of file From d6120ed1b568e5588a32bbc3c421b378c9ab9666 Mon Sep 17 00:00:00 2001 From: sanger-tolsoft <105875386+sanger-tolsoft@users.noreply.github.com> Date: Fri, 4 Apr 2025 09:28:17 +0000 Subject: [PATCH 3/5] Template update for nf-core/tools version 3.2.0 --- .nf-core.yml | 54 +++++++++++++++++++++--------------------- ro-crate-metadata.json | 42 ++++++++++---------------------- 2 files changed, 40 insertions(+), 56 deletions(-) diff --git a/.nf-core.yml b/.nf-core.yml index 05668f74..4d1ee8ee 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -1,35 +1,35 @@ lint: files_exist: - - CODE_OF_CONDUCT.md - - assets/nf-core-blobtoolkit_logo_light.png - - docs/images/nf-core-blobtoolkit_logo_light.png - - docs/images/nf-core-blobtoolkit_logo_dark.png - - .github/ISSUE_TEMPLATE/config.yml - - .github/workflows/awstest.yml - - .github/workflows/awsfulltest.yml - - conf/igenomes.config + - CODE_OF_CONDUCT.md + - assets/nf-core-blobtoolkit_logo_light.png + - docs/images/nf-core-blobtoolkit_logo_light.png + - docs/images/nf-core-blobtoolkit_logo_dark.png + - .github/ISSUE_TEMPLATE/config.yml + - .github/workflows/awstest.yml + - .github/workflows/awsfulltest.yml + - conf/igenomes.config files_unchanged: - - LICENCE - - lib/NfcoreTemplate.groovy - - CODE_OF_CONDUCT.md - - assets/sendmail_template.txt - - assets/email_template.html - - assets/email_template.txt - - assets/nf-core-blobtoolkit_logo_light.png - - docs/images/nf-core-blobtoolkit_logo_light.png - - docs/images/nf-core-blobtoolkit_logo_dark.png - - .github/ISSUE_TEMPLATE/bug_report.yml - - .github/PULL_REQUEST_TEMPLATE.md - - .github/workflows/linting.yml - - .github/workflows/branch.yml - - .github/CONTRIBUTING.md - - .github/workflows/linting_comment.yml + - LICENCE + - lib/NfcoreTemplate.groovy + - CODE_OF_CONDUCT.md + - assets/sendmail_template.txt + - assets/email_template.html + - assets/email_template.txt + - assets/nf-core-blobtoolkit_logo_light.png + - docs/images/nf-core-blobtoolkit_logo_light.png + - docs/images/nf-core-blobtoolkit_logo_dark.png + - .github/ISSUE_TEMPLATE/bug_report.yml + - .github/PULL_REQUEST_TEMPLATE.md + - .github/workflows/linting.yml + - .github/workflows/branch.yml + - .github/CONTRIBUTING.md + - .github/workflows/linting_comment.yml merge_markers: false multiqc_config: - - report_comment + - report_comment nextflow_config: - - manifest.name - - manifest.homePage + - manifest.name + - manifest.homePage template_strings: false nf_core_version: 3.2.0 repository_type: pipeline @@ -42,5 +42,5 @@ template: org: sanger-tol outdir: . skip_features: - - igenomes + - igenomes version: 0.7.1 diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json index db1d55b1..66e0bff8 100644 --- a/ro-crate-metadata.json +++ b/ro-crate-metadata.json @@ -22,7 +22,7 @@ "@id": "./", "@type": "Dataset", "creativeWorkStatus": "Stable", - "datePublished": "2025-04-03T19:22:00+00:00", + "datePublished": "2025-04-04T09:28:12+00:00", "description": "# sanger-tol/blobtoolkit\n\n[![GitHub Actions CI Status](https://github.com/sanger-tol/blobtoolkit/actions/workflows/ci.yml/badge.svg)](https://github.com/sanger-tol/blobtoolkit/actions/workflows/ci.yml)\n[![GitHub Actions Linting Status](https://github.com/sanger-tol/blobtoolkit/actions/workflows/linting.yml/badge.svg)](https://github.com/sanger-tol/blobtoolkit/actions/workflows/linting.yml)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)\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/nextflow%20DSL2-%E2%89%A524.04.2-23aa62.svg)](https://www.nextflow.io/)\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/sanger-tol/blobtoolkit)\n\n## Introduction\n\n**sanger-tol/blobtoolkit** is a bioinformatics pipeline that ...\n\n\n\n\n1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))\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\n\n\nNow, you can run the pipeline using:\n\n\n\n```bash\nnextflow run sanger-tol/blobtoolkit \\\n -profile \\\n --input samplesheet.csv \\\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\n## Credits\n\nsanger-tol/blobtoolkit was originally written by priyanka-surana.\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).\n\n## Citations\n\n\n\n\n\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nThis pipeline uses code and infrastructure developed and maintained by the [nf-core](https://nf-co.re) community, reused here under the [MIT license](https://github.com/nf-core/tools/blob/main/LICENSE).\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n", "hasPart": [ { @@ -93,7 +93,7 @@ }, "mentions": [ { - "@id": "#040370e7-e13b-4de6-9268-07dc566af218" + "@id": "#b0ae3275-3474-4067-9286-27deaa3ab943" } ], "name": "sanger-tol/blobtoolkit" @@ -115,11 +115,7 @@ }, { "@id": "main.nf", - "@type": [ - "File", - "SoftwareSourceCode", - "ComputationalWorkflow" - ], + "@type": ["File", "SoftwareSourceCode", "ComputationalWorkflow"], "creator": [ { "@id": "https://orcid.org/0000-0002-7860-3560" @@ -129,31 +125,19 @@ } ], "dateCreated": "", - "dateModified": "2025-04-03T19:22:00Z", + "dateModified": "2025-04-04T09:28:12Z", "dct:conformsTo": "https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE/", - "keywords": [ - "nf-core", - "nextflow" - ], - "license": [ - "MIT" - ], - "name": [ - "sanger-tol/blobtoolkit" - ], + "keywords": ["nf-core", "nextflow"], + "license": ["MIT"], + "name": ["sanger-tol/blobtoolkit"], "programmingLanguage": { "@id": "https://w3id.org/workflowhub/workflow-ro-crate#nextflow" }, "sdPublisher": { "@id": "https://nf-co.re/" }, - "url": [ - "https://github.com/sanger-tol/blobtoolkit", - "https://nf-co.re/sanger-tol/blobtoolkit/0.7.1/" - ], - "version": [ - "0.7.1" - ] + "url": ["https://github.com/sanger-tol/blobtoolkit", "https://nf-co.re/sanger-tol/blobtoolkit/0.7.1/"], + "version": ["0.7.1"] }, { "@id": "https://w3id.org/workflowhub/workflow-ro-crate#nextflow", @@ -168,11 +152,11 @@ "version": "!>=24.04.2" }, { - "@id": "#040370e7-e13b-4de6-9268-07dc566af218", + "@id": "#b0ae3275-3474-4067-9286-27deaa3ab943", "@type": "TestSuite", "instance": [ { - "@id": "#1489a662-31a8-4c51-92a7-bada870a94dd" + "@id": "#45472d46-a8b9-4e35-a5fe-d664b7f7b307" } ], "mainEntity": { @@ -181,7 +165,7 @@ "name": "Test suite for sanger-tol/blobtoolkit" }, { - "@id": "#1489a662-31a8-4c51-92a7-bada870a94dd", + "@id": "#45472d46-a8b9-4e35-a5fe-d664b7f7b307", "@type": "TestInstance", "name": "GitHub Actions workflow for testing sanger-tol/blobtoolkit", "resource": "repos/sanger-tol/blobtoolkit/actions/workflows/ci.yml", @@ -312,4 +296,4 @@ "name": "Priyanka Surana" } ] -} \ No newline at end of file +} From 014b3267e6638f1f6e41eacfce1a09b6d8611e80 Mon Sep 17 00:00:00 2001 From: Tyler Chafin Date: Sun, 6 Apr 2025 15:15:31 +0100 Subject: [PATCH 4/5] Move CI to use miniprot (#160) * Move CI to use miniprot * use metaeuk for non-test runs * Removed extra whitespace * Removed comment that applied to metaeuk * Removed extra whitespace --------- Co-authored-by: Matthieu Muffato --- conf/modules.config | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/conf/modules.config b/conf/modules.config index 3bb93339..a9605748 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -86,10 +86,8 @@ process { // Obey "use_work_dir_as_temp", except for large genomes scratch = { !params.use_work_dir_as_temp || (meta.genome_size < 2000000000) } ext.args = { 'test' in workflow.profile.tokenize(',') || 'test_raw' in workflow.profile.tokenize(',') || 'test_nobusco' in workflow.profile.tokenize(',') ? - // Additional configuration to speed processes up during testing. - // Note: BUSCO *must* see the double-quotes around the parameters - '--force --metaeuk --metaeuk_parameters \'"-s=2"\' --metaeuk_rerun_parameters \'"-s=2"\'' - : '--force --metaeuk' } + '--force' // Runs with miniprot + : '--force --metaeuk' } } withName: "RESTRUCTUREBUSCODIR" { From 176d244b8a05e61e328e87cc9d612d018d3d2216 Mon Sep 17 00:00:00 2001 From: Guoying Qi <729395+gq1@users.noreply.github.com> Date: Mon, 14 Apr 2025 09:41:46 +0100 Subject: [PATCH 5/5] Update branch.yml --- .github/workflows/branch.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/branch.yml b/.github/workflows/branch.yml index e342b98e..9f9c5568 100644 --- a/.github/workflows/branch.yml +++ b/.github/workflows/branch.yml @@ -12,6 +12,7 @@ jobs: runs-on: ubuntu-latest steps: # PRs to the nf-core repo main/master branch are only ok if coming from the nf-core repo `dev` or any `patch` branches + # Testing here - name: Check PRs if: github.repository == 'sanger-tol/blobtoolkit' run: |