diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml
index c44cd332a..5a98c9fde 100644
--- a/.github/workflows/awsfulltest.yml
+++ b/.github/workflows/awsfulltest.yml
@@ -4,44 +4,23 @@ name: nf-core AWS full size tests
# It runs the -profile 'test_full' on AWS batch
on:
- pull_request:
- branches:
- - main
- - master
workflow_dispatch:
pull_request_review:
types: [submitted]
+ release:
+ types: [published]
jobs:
run-platform:
name: Run AWS full tests
- # run only if the PR is approved by at least 2 reviewers and against the master branch or manually triggered
- if: github.repository == 'nf-core/rnaseq' && github.event.review.state == 'approved' && github.event.pull_request.base.ref == 'master' || github.event_name == 'workflow_dispatch'
+ # run only if the PR is approved by at least 2 reviewers and against the master/main branch or manually triggered
+ if: github.repository == 'nf-core/rnaseq' && github.event.review.state == 'approved' && (github.event.pull_request.base.ref == 'master' || github.event.pull_request.base.ref == 'main') || github.event_name == 'workflow_dispatch'
runs-on: ubuntu-latest
steps:
- - name: Get PR reviews
- uses: octokit/request-action@v2.x
- if: github.event_name != 'workflow_dispatch'
- id: check_approvals
- continue-on-error: true
- with:
- route: GET /repos/${{ github.repository }}/pulls/${{ github.event.pull_request.number }}/reviews?per_page=100
- env:
- GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-
- - name: Check for approvals
- if: ${{ failure() && github.event_name != 'workflow_dispatch' }}
- run: |
- echo "No review approvals found. At least 2 approvals are required to run this action automatically."
- exit 1
-
- - name: Check for enough approvals (>=2)
- id: test_variables
- if: github.event_name != 'workflow_dispatch'
+ - name: Set revision variable
+ id: revision
run: |
- JSON_RESPONSE='${{ steps.check_approvals.outputs.data }}'
- CURRENT_APPROVALS_COUNT=$(echo $JSON_RESPONSE | jq -c '[.[] | select(.state | contains("APPROVED")) ] | length')
- test $CURRENT_APPROVALS_COUNT -ge 2 || exit 1 # At least 2 approvals are required
+ echo "revision=${{ (github.event_name == 'workflow_dispatch' || github.event_name == 'release') && github.sha || 'dev' }}" >> "$GITHUB_OUTPUT"
- name: Launch workflow via Seqera Platform
uses: seqeralabs/action-tower-launch@v2
@@ -52,12 +31,12 @@ jobs:
workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
compute_env: ${{ secrets.TOWER_COMPUTE_ENV }}
- revision: ${{ github.sha }}
- workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/rnaseq/work-${{ github.sha }}
+ revision: ${{ steps.revision.outputs.revision }}
+ workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/rnaseq/work-${{ steps.revision.outputs.revision }}
parameters: |
{
"hook_url": "${{ secrets.MEGATESTS_ALERTS_SLACK_HOOK_URL }}",
- "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/rnaseq/results-${{ github.sha }}"
+ "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/rnaseq/results-${{ steps.revision.outputs.revision }}"
}
profiles: test_full
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 4a4e5fac6..2a764926c 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -83,5 +83,6 @@ jobs:
uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
- name: "Run pipeline with test data ${{ matrix.NXF_VER }} | ${{ matrix.test_name }} | ${{ matrix.profile }}"
+ continue-on-error: ${{ matrix.NXF_VER == 'latest-everything' }}
run: |
nextflow run ${GITHUB_WORKSPACE} -profile ${{ matrix.test_name }},${{ matrix.profile }} --outdir ./results
diff --git a/.nf-core.yml b/.nf-core.yml
index 97dadc8dd..65b7e4b50 100644
--- a/.nf-core.yml
+++ b/.nf-core.yml
@@ -11,7 +11,7 @@ lint:
nextflow_config:
- config_defaults:
- params.ribo_database_manifest
-nf_core_version: 3.2.0
+nf_core_version: 3.2.1
repository_type: pipeline
template:
author: "Harshil Patel, Phil Ewels, Rickard Hammar\xE9n"
diff --git a/nextflow.config b/nextflow.config
index 916d064b6..beaf97328 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -265,7 +265,7 @@ manifest {
// Nextflow plugins
plugins {
- id 'nf-schema@2.3.0' // Validation of pipeline parameters and creation of an input channel from a sample sheet
+ id 'nf-schema@2.2.0' // Validation of pipeline parameters and creation of an input channel from a sample sheet
}
validation {
diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json
index 2808958e8..d6d733a66 100644
--- a/ro-crate-metadata.json
+++ b/ro-crate-metadata.json
@@ -22,7 +22,7 @@
"@id": "./",
"@type": "Dataset",
"creativeWorkStatus": "InProgress",
- "datePublished": "2025-01-27T14:47:16+00:00",
+ "datePublished": "2025-04-30T12:27:54+00:00",
"description": "
\n \n \n \n \n
\n\n[](https://github.com/nf-core/rnaseq/actions/workflows/ci.yml)\n[](https://github.com/nf-core/rnaseq/actions/workflows/linting.yml)[](https://nf-co.re/rnaseq/results)[](https://doi.org/10.5281/zenodo.XXXXXXX)\n[](https://www.nf-test.com)\n\n[](https://www.nextflow.io/)\n[](https://docs.conda.io/en/latest/)\n[](https://www.docker.com/)\n[](https://sylabs.io/docs/)\n[](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/rnaseq)\n\n[](https://nfcore.slack.com/channels/rnaseq)[](https://twitter.com/nf_core)[](https://mstdn.science/@nf_core)[](https://www.youtube.com/c/nf-core)\n\n## Introduction\n\n**nf-core/rnaseq** 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 nf-core/rnaseq \\\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\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/rnaseq/usage) and the [parameter documentation](https://nf-co.re/rnaseq/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/rnaseq/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/rnaseq/output).\n\n## Credits\n\nnf-core/rnaseq was originally written by Harshil Patel, Phil Ewels, Rickard Hammar\u00e9n.\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\nFor further information or help, don't hesitate to get in touch on the [Slack `#rnaseq` channel](https://nfcore.slack.com/channels/rnaseq) (you can join with [this invite](https://nf-co.re/join/slack)).\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\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": [
{
@@ -99,7 +99,7 @@
},
"mentions": [
{
- "@id": "#0bb8ad79-8c56-4c40-8c8f-3f3a759cb012"
+ "@id": "#cd43f0fe-3ad6-4bc1-8cfb-75fa28b1a984"
}
],
"name": "nf-core/rnaseq"
@@ -128,7 +128,7 @@
}
],
"dateCreated": "",
- "dateModified": "2025-01-27T14:47:16Z",
+ "dateModified": "2025-04-30T12:27:54Z",
"dct:conformsTo": "https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE/",
"keywords": ["nf-core", "nextflow", "rna", "rna-seq"],
"license": ["MIT"],
@@ -160,11 +160,11 @@
"version": "!>=24.04.2"
},
{
- "@id": "#0bb8ad79-8c56-4c40-8c8f-3f3a759cb012",
+ "@id": "#cd43f0fe-3ad6-4bc1-8cfb-75fa28b1a984",
"@type": "TestSuite",
"instance": [
{
- "@id": "#23a449b9-016a-4957-a48a-d2dc5dc0b823"
+ "@id": "#26d6a15d-107f-4ba0-b65e-85004e2a79f1"
}
],
"mainEntity": {
@@ -173,7 +173,7 @@
"name": "Test suite for nf-core/rnaseq"
},
{
- "@id": "#23a449b9-016a-4957-a48a-d2dc5dc0b823",
+ "@id": "#26d6a15d-107f-4ba0-b65e-85004e2a79f1",
"@type": "TestInstance",
"name": "GitHub Actions workflow for testing nf-core/rnaseq",
"resource": "repos/nf-core/rnaseq/actions/workflows/ci.yml",
![\"nf-core/rnaseq\"](\"docs/images/nf-core-rnaseq_logo_dark.png\"){kind=logo}
\n