Default branch change

.github/PULL_REQUEST_TEMPLATE.md

@@ -8,14 +8,14 @@ These are the most common things requested on pull requests (PRs).
 
 Remember that PRs should be made against the dev branch, unless you're preparing a pipeline release.
 
-Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/denovotranscript/tree/master/.github/CONTRIBUTING.md)
+Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/denovotranscript/tree/main/.github/CONTRIBUTING.md)
 -->
 
 ## PR checklist
 
 - [ ] This comment contains a description of changes (with reason).
 - [ ] If you've fixed a bug or added code that should be tested, add tests!
-- [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/denovotranscript/tree/master/.github/CONTRIBUTING.md)
+- [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/denovotranscript/tree/main/.github/CONTRIBUTING.md)
 - [ ] If necessary, also make a PR on the nf-core/denovotranscript _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository.
 - [ ] Make sure your code lints (`nf-core pipelines lint`).
 - [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --outdir <OUTDIR>`).

.nf-core.yml

@@ -1,4 +1,6 @@
 lint:
+  files_unchanged:
+    - .github/PULL_REQUEST_TEMPLATE.md
   nextflow_config:
     - config_defaults:
         - params.ribo_database_manifest

CHANGELOG.md

@@ -5,6 +5,9 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## v1.3.0dev - [date]
 
+### `Changed`
+
+- [PR #43](https://github.com/nf-core/denovotranscript/pull/43) - Default branch changed from `master` to `main` (by @vagkaratzas)
 - [PR #37](https://github.com/nf-core/denovotranscript/pull/37) - Bump version to 1.3.0dev
 
 ## v1.2.0 - [2025-01-30]

assets/schema_input.json

@@ -1,6 +1,6 @@
 {
     "$schema": "https://json-schema.org/draft/2020-12/schema",
-    "$id": "https://raw.githubusercontent.com/nf-core/denovotranscript/master/assets/schema_input.json",
+    "$id": "https://raw.githubusercontent.com/nf-core/denovotranscript/main/assets/schema_input.json",
     "title": "nf-core/denovotranscript pipeline - params.input schema",
     "description": "Schema for the file provided with params.input",
     "type": "array",

nextflow.config

@@ -289,7 +289,7 @@ manifest {
     homePage        = 'https://github.com/nf-core/denovotranscript'
     description     = """A pipeline for de novo transcriptome assembly of short reads from bulk RNA-seq"""
     mainScript      = 'main.nf'
-    defaultBranch   = 'master'
+    defaultBranch   = 'main'
     nextflowVersion = '!>=24.04.2'
     version         = '1.3.0dev'
     doi             = '10.5281/zenodo.13324371'
@@ -323,7 +323,7 @@ validation {
     https://doi.org/10.1038/s41587-020-0439-x
 
 * Software dependencies
-    https://github.com/nf-core/denovotranscript/blob/master/CITATIONS.md
+    https://github.com/nf-core/denovotranscript/blob/main/CITATIONS.md
 """
     }
     summary {

nextflow_schema.json

@@ -1,6 +1,6 @@
 {
     "$schema": "https://json-schema.org/draft/2020-12/schema",
-    "$id": "https://raw.githubusercontent.com/nf-core/denovotranscript/master/nextflow_schema.json",
+    "$id": "https://raw.githubusercontent.com/nf-core/denovotranscript/main/nextflow_schema.json",
     "title": "nf-core/denovotranscript pipeline parameters",
     "description": "A pipeline for de novo transcriptome assembly of short reads from bulk RNA-seq",
     "type": "object",

ro-crate-metadata.json

@@ -22,7 +22,7 @@
             "@id": "./",
             "@type": "Dataset",
             "creativeWorkStatus": "InProgress",
-            "datePublished": "2025-04-30T12:25:59+00:00",
+            "datePublished": "2025-05-23T09:44:35+00:00",
             "description": "<h1>\n  <picture>\n    <source media=\"(prefers-color-scheme: dark)\" srcset=\"docs/images/nf-core-denovotranscript_logo_dark.png\">\n    <img alt=\"nf-core/denovotranscript\" src=\"docs/images/nf-core-denovotranscript_logo_light.png\">\n  </picture>\n</h1>\n\n[![GitHub Actions CI Status](https://github.com/nf-core/denovotranscript/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-core/denovotranscript/actions/workflows/ci.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/denovotranscript/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/denovotranscript/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/denovotranscript/results)[![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/nf-core/denovotranscript)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23denovotranscript-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/denovotranscript)[![Follow on Twitter](http://img.shields.io/badge/twitter-%40nf__core-1DA1F2?labelColor=000000&logo=twitter)](https://twitter.com/nf_core)[![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/denovotranscript** 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 nf-core/denovotranscript \\\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\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/denovotranscript/usage) and the [parameter documentation](https://nf-co.re/denovotranscript/parameters).\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/denovotranscript/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/denovotranscript/output).\n\n## Credits\n\nnf-core/denovotranscript was originally written by Avani Bhojwani and Timothy Little.\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\nFor further information or help, don't hesitate to get in touch on the [Slack `#denovotranscript` channel](https://nfcore.slack.com/channels/denovotranscript) (you can join with [this invite](https://nf-co.re/join/slack)).\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 nf-core/denovotranscript 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\nYou can cite the `nf-core` publication as follows:\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": [
                 {
@@ -102,7 +102,7 @@
             },
             "mentions": [
                 {
-                    "@id": "#27e4031e-7bf9-4d01-8778-a6b33b556e4e"
+                    "@id": "#b5d8f586-3a26-429d-b9bb-686a7236d515"
                 }
             ],
             "name": "nf-core/denovotranscript"
@@ -130,7 +130,7 @@
                 "ComputationalWorkflow"
             ],
             "dateCreated": "",
-            "dateModified": "2025-04-30T12:25:59Z",
+            "dateModified": "2025-05-23T10:44:35Z",
             "dct:conformsTo": "https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE/",
             "keywords": [
                 "nf-core",
@@ -151,8 +151,13 @@
             "sdPublisher": {
                 "@id": "https://nf-co.re/"
             },
-            "url": ["https://github.com/nf-core/denovotranscript", "https://nf-co.re/denovotranscript/dev/"],
-            "version": ["1.3.0dev"]
+            "url": [
+                "https://github.com/nf-core/denovotranscript",
+                "https://nf-co.re/denovotranscript/dev/"
+            ],
+            "version": [
+                "1.3.0dev"
+            ]
         },
         {
             "@id": "https://w3id.org/workflowhub/workflow-ro-crate#nextflow",
@@ -167,11 +172,11 @@
             "version": "!>=24.04.2"
         },
         {
-            "@id": "#27e4031e-7bf9-4d01-8778-a6b33b556e4e",
+            "@id": "#b5d8f586-3a26-429d-b9bb-686a7236d515",
             "@type": "TestSuite",
             "instance": [
                 {
-                    "@id": "#c17d261d-a145-44fa-8991-9c5542d56361"
+                    "@id": "#67881ca6-82d7-42ea-adf8-1155f43b711a"
                 }
             ],
             "mainEntity": {
@@ -180,7 +185,7 @@
             "name": "Test suite for nf-core/denovotranscript"
         },
         {
-            "@id": "#c17d261d-a145-44fa-8991-9c5542d56361",
+            "@id": "#67881ca6-82d7-42ea-adf8-1155f43b711a",
             "@type": "TestInstance",
             "name": "GitHub Actions workflow for testing nf-core/denovotranscript",
             "resource": "repos/nf-core/denovotranscript/actions/workflows/ci.yml",