Testing ci

.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: |

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 The pipeline has now been validated for draft (unpublished) assemblies.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

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" {

ro-crate-metadata.json

@@ -22,7 +22,7 @@
             "@id": "./",
             "@type": "Dataset",
             "creativeWorkStatus": "Stable",
-            "datePublished": "2025-03-07T13:35:10+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<!-- TODO nf-core:\n   Complete this sentence with a 2-3 sentence summary of what types of data the pipeline ingests, a brief overview of the\n   major pipeline sections and the types of output it produces. You're giving an overview to someone new\n   to nf-core here, in 15-20 seconds. For an example, see https://github.com/nf-core/rnaseq/blob/master/README.md#introduction\n-->\n\n<!-- TODO nf-core: Include a figure that guides the user through the major workflow steps. Many nf-core\n     workflows use the \"tube map\" design for that. See https://nf-co.re/docs/contributing/design_guidelines#examples for examples.   -->\n<!-- TODO nf-core: Fill in short bullet-pointed list of the default steps in the pipeline -->1. 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<!-- TODO nf-core: Describe the minimum required steps to execute the pipeline, e.g. how to prepare samplesheets.\n     Explain what rows and columns represent. For instance (please edit as appropriate):\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\nCONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz\n```\n\nEach row represents a fastq file (single-end) or a pair of fastq files (paired end).\n\n-->\n\nNow, you can run the pipeline using:\n\n<!-- TODO nf-core: update the following command to include all required parameters for a minimal example -->\n\n```bash\nnextflow run sanger-tol/blobtoolkit \\\n   -profile <docker/singularity/.../institute> \\\n   --input samplesheet.csv \\\n   --outdir <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<!-- TODO nf-core: If applicable, make list of people who have also contributed -->\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<!-- TODO nf-core: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file. -->\n<!-- If you use sanger-tol/blobtoolkit for your analysis, please cite it using the following doi: [10.5281/zenodo.XXXXXX](https://doi.org/10.5281/zenodo.XXXXXX) -->\n\n<!-- TODO nf-core: Add bibliography of tools and data used in your pipeline -->\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": "#b0ae3275-3474-4067-9286-27deaa3ab943"
                 }
             ],
             "name": "sanger-tol/blobtoolkit"
@@ -115,45 +115,29 @@
         },
         {
             "@id": "main.nf",
-            "@type": [
-                "File",
-                "SoftwareSourceCode",
-                "ComputationalWorkflow"
-            ],
+            "@type": ["File", "SoftwareSourceCode", "ComputationalWorkflow"],
             "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": "2025-04-04T09:28:12Z",
             "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": "#8275489f-2726-4d94-b502-adfbd72b7b9d",
+            "@id": "#b0ae3275-3474-4067-9286-27deaa3ab943",
             "@type": "TestSuite",
             "instance": [
                 {
-                    "@id": "#c10b809d-8e67-421b-acff-2c4de88bcf1f"
+                    "@id": "#45472d46-a8b9-4e35-a5fe-d664b7f7b307"
                 }
             ],
             "mainEntity": {
@@ -181,7 +165,7 @@
             "name": "Test suite for sanger-tol/blobtoolkit"
         },
         {
-            "@id": "#c10b809d-8e67-421b-acff-2c4de88bcf1f",
+            "@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",
@@ -299,17 +283,17 @@
             "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"
         }
     ]
-}
+}