diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 736f66c..ee9b579 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -46,6 +46,8 @@ jobs: steps: - name: Check out pipeline code uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4 + with: + fetch-depth: 0 - name: Set up Nextflow uses: nf-core/setup-nextflow@v2 diff --git a/.github/workflows/download_pipeline.yml b/.github/workflows/download_pipeline.yml index 13b51e2..ab06316 100644 --- a/.github/workflows/download_pipeline.yml +++ b/.github/workflows/download_pipeline.yml @@ -34,6 +34,17 @@ jobs: REPO_LOWERCASE: ${{ steps.get_repo_properties.outputs.REPO_LOWERCASE }} REPOTITLE_LOWERCASE: ${{ steps.get_repo_properties.outputs.REPOTITLE_LOWERCASE }} REPO_BRANCH: ${{ steps.get_repo_properties.outputs.REPO_BRANCH }} + steps: + - name: Get the repository name and current branch + id: get_repo_properties + run: | + echo "REPO_LOWERCASE=${GITHUB_REPOSITORY,,}" >> "$GITHUB_OUTPUT" + echo "REPOTITLE_LOWERCASE=$(basename ${GITHUB_REPOSITORY,,})" >> "$GITHUB_OUTPUT" + echo "REPO_BRANCH=${{ github.event.inputs.testbranch || 'dev' }}" >> "$GITHUB_OUTPUT" + + download: + runs-on: ubuntu-latest + needs: configure steps: - name: Install Nextflow uses: nf-core/setup-nextflow@v2 @@ -56,21 +67,10 @@ jobs: python -m pip install --upgrade pip pip install git+https://github.com/nf-core/tools.git@dev - - name: Get the repository name and current branch set as environment variable - id: get_repo_properties - run: | - echo "REPO_LOWERCASE=${GITHUB_REPOSITORY,,}" >> "$GITHUB_OUTPUT" - echo "REPOTITLE_LOWERCASE=$(basename ${GITHUB_REPOSITORY,,})" >> "$GITHUB_OUTPUT" - echo "REPO_BRANCH=${{ github.event.inputs.testbranch || 'dev' }}" >> "$GITHUB_OUTPUT" - - name: Make a cache directory for the container images run: | mkdir -p ./singularity_container_images - download: - runs-on: ubuntu-latest - needs: configure - steps: - name: Download the pipeline env: NXF_SINGULARITY_CACHEDIR: ./singularity_container_images @@ -87,6 +87,9 @@ jobs: - name: Inspect download run: tree ./${{ needs.configure.outputs.REPOTITLE_LOWERCASE }} + - name: Inspect container images + run: tree ./singularity_container_images | tee ./container_initial + - name: Count the downloaded number of container images id: count_initial run: | @@ -123,7 +126,8 @@ jobs: final_count=${{ steps.count_afterwards.outputs.IMAGE_COUNT_AFTER }} difference=$((final_count - initial_count)) echo "$difference additional container images were \n downloaded at runtime . The pipeline has no support for offline runs!" - tree ./singularity_container_images + tree ./singularity_container_images > ./container_afterwards + diff ./container_initial ./container_afterwards exit 1 else echo "The pipeline can be downloaded successfully!" diff --git a/.github/workflows/linting_comment.yml b/.github/workflows/linting_comment.yml index 0bed96d..95b6b6a 100644 --- a/.github/workflows/linting_comment.yml +++ b/.github/workflows/linting_comment.yml @@ -11,7 +11,7 @@ jobs: runs-on: ubuntu-latest steps: - name: Download lint results - uses: dawidd6/action-download-artifact@80620a5d27ce0ae443b965134db88467fc607b43 # v7 + uses: dawidd6/action-download-artifact@20319c5641d495c8a52e688b7dc5fada6c3a9fbc # v8 with: workflow: linting.yml workflow_conclusion: completed diff --git a/.github/workflows/release-announcements.yml b/.github/workflows/release-announcements.yml index 450b1d5..76a9e67 100644 --- a/.github/workflows/release-announcements.yml +++ b/.github/workflows/release-announcements.yml @@ -27,39 +27,6 @@ jobs: ${{ steps.get_topics.outputs.topics }} #nfcore #openscience #nextflow #bioinformatics - send-tweet: - runs-on: ubuntu-latest - - steps: - - uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5 - with: - python-version: "3.10" - - name: Install dependencies - run: pip install tweepy==4.14.0 - - name: Send tweet - shell: python - run: | - import os - import tweepy - - client = tweepy.Client( - access_token=os.getenv("TWITTER_ACCESS_TOKEN"), - access_token_secret=os.getenv("TWITTER_ACCESS_TOKEN_SECRET"), - consumer_key=os.getenv("TWITTER_CONSUMER_KEY"), - consumer_secret=os.getenv("TWITTER_CONSUMER_SECRET"), - ) - tweet = os.getenv("TWEET") - client.create_tweet(text=tweet) - env: - TWEET: | - Pipeline release! ${{ github.repository }} v${{ github.event.release.tag_name }} - ${{ github.event.release.name }}! - - Please see the changelog: ${{ github.event.release.html_url }} - TWITTER_CONSUMER_KEY: ${{ secrets.TWITTER_CONSUMER_KEY }} - TWITTER_CONSUMER_SECRET: ${{ secrets.TWITTER_CONSUMER_SECRET }} - TWITTER_ACCESS_TOKEN: ${{ secrets.TWITTER_ACCESS_TOKEN }} - TWITTER_ACCESS_TOKEN_SECRET: ${{ secrets.TWITTER_ACCESS_TOKEN_SECRET }} - bsky-post: runs-on: ubuntu-latest steps: diff --git a/.nf-core.yml b/.nf-core.yml index b233b9a..135705f 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -9,7 +9,7 @@ lint: multiqc_config: false nextflow_config: - params.input -nf_core_version: 3.1.1 +nf_core_version: 3.2.0 repository_type: pipeline template: author: Judith Bernett diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 9e9f0e1..1dec865 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -7,7 +7,7 @@ repos: - prettier@3.2.5 - repo: https://github.com/editorconfig-checker/editorconfig-checker.python - rev: "3.0.3" + rev: "3.1.2" hooks: - id: editorconfig-checker alias: ec diff --git a/README.md b/README.md index 7a975a1..7676837 100644 --- a/README.md +++ b/README.md @@ -3,7 +3,9 @@ nf-core/drugresponseeval -[![GitHub Actions CI Status](https://github.com/nf-core/drugresponseeval/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-core/drugresponseeval/actions/workflows/ci.yml) + + +[![GitHub Actions CI Status](https://github.com/nf-core/drugresponseeval/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-core/drugresponseeval/actions/workflows/ci.yml) [![GitHub Actions Linting Status](https://github.com/nf-core/drugresponseeval/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/drugresponseeval/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/drugresponseeval/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX) [![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com) @@ -49,7 +51,7 @@ For baseline models, no randomization or robustness tests are performed. ## Usage > [!NOTE] -> 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. +> 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. Now, you can run the pipeline using: @@ -95,7 +97,9 @@ For further information or help, don't hesitate to get in touch on the [Slack `# ## Citations - + + + An extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file. diff --git a/nextflow.config b/nextflow.config index 1fe0791..2c0f9e3 100644 --- a/nextflow.config +++ b/nextflow.config @@ -202,14 +202,14 @@ env { } // Set bash options -process.shell = """\ -bash - -set -e # Exit if a tool returns a non-zero status/exit code -set -u # Treat unset variables and parameters as an error -set -o pipefail # Returns the status of the last command to exit with a non-zero status or zero if all successfully execute -set -C # No clobber - prevent output redirection from overwriting files. -""" +process.shell = [ + "bash", + "-C", // No clobber - prevent output redirection from overwriting files. + "-e", // Exit if a tool returns a non-zero status/exit code + "-u", // Treat unset variables and parameters as an error + "-o", // Returns the status of the last command to exit.. + "pipefail" // ..with a non-zero status or zero if all successfully execute +] // Disable process selector warnings by default. Use debug profile to enable warnings. nextflow.enable.configProcessNamesValidation = false @@ -256,7 +256,7 @@ manifest { // Nextflow plugins plugins { - id 'nf-schema@2.1.1' // Validation of pipeline parameters and creation of an input channel from a sample sheet + id 'nf-schema@2.3.0' // 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 47066e1..aef43fc 100644 --- a/ro-crate-metadata.json +++ b/ro-crate-metadata.json @@ -22,8 +22,8 @@ "@id": "./", "@type": "Dataset", "creativeWorkStatus": "InProgress", - "datePublished": "2024-12-20T13:09:20+00:00", - "description": "

\n \n \n \"nf-core/drugresponseeval\"\n \n

[![GitHub Actions CI Status](https://github.com/nf-core/drugresponseeval/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-core/drugresponseeval/actions/workflows/ci.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/drugresponseeval/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/drugresponseeval/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/drugresponseeval/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/drugresponseeval)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23drugresponseeval-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/drugresponseeval)[![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/drugresponseeval** is a bioinformatics pipeline that ...\n\n\n\n\n\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/drugresponseeval \\\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/drugresponseeval/usage) and the [parameter documentation](https://nf-co.re/drugresponseeval/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/drugresponseeval/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/drugresponseeval/output).\n\n## Credits\n\nnf-core/drugresponseeval was originally written by Judith Bernett.\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 `#drugresponseeval` channel](https://nfcore.slack.com/channels/drugresponseeval) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\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", + "datePublished": "2025-01-27T14:45:31+00:00", + "description": "

\n \n \n \"nf-core/drugresponseeval\"\n \n

\n\n[![GitHub Actions CI Status](https://github.com/nf-core/drugresponseeval/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-core/drugresponseeval/actions/workflows/ci.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/drugresponseeval/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/drugresponseeval/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/drugresponseeval/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/drugresponseeval)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23drugresponseeval-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/drugresponseeval)[![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/drugresponseeval** is a bioinformatics pipeline that ...\n\n\n\n\n\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/drugresponseeval \\\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/drugresponseeval/usage) and the [parameter documentation](https://nf-co.re/drugresponseeval/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/drugresponseeval/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/drugresponseeval/output).\n\n## Credits\n\nnf-core/drugresponseeval was originally written by Judith Bernett.\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 `#drugresponseeval` channel](https://nfcore.slack.com/channels/drugresponseeval) (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": [ { "@id": "main.nf" @@ -93,7 +93,7 @@ }, "mentions": [ { - "@id": "#ac53992c-1e82-45a6-9090-78a775a22a67" + "@id": "#859e0da7-cdd6-48e5-8a21-9be134a786bc" } ], "name": "nf-core/drugresponseeval" @@ -115,18 +115,14 @@ }, { "@id": "main.nf", - "@type": [ - "File", - "SoftwareSourceCode", - "ComputationalWorkflow" - ], + "@type": ["File", "SoftwareSourceCode", "ComputationalWorkflow"], "creator": [ { "@id": "https://orcid.org/0000-0001-5812-8013" } ], "dateCreated": "", - "dateModified": "2024-12-20T13:09:20Z", + "dateModified": "2025-01-27T14:45:31Z", "dct:conformsTo": "https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE/", "keywords": [ "nf-core", @@ -145,30 +141,21 @@ "robustness-assessment", "training" ], - "license": [ - "MIT" - ], + "license": ["MIT"], "maintainer": [ { "@id": "https://orcid.org/0000-0001-5812-8013" } ], - "name": [ - "nf-core/drugresponseeval" - ], + "name": ["nf-core/drugresponseeval"], "programmingLanguage": { "@id": "https://w3id.org/workflowhub/workflow-ro-crate#nextflow" }, "sdPublisher": { "@id": "https://nf-co.re/" }, - "url": [ - "https://github.com/nf-core/drugresponseeval", - "https://nf-co.re/drugresponseeval/dev/" - ], - "version": [ - "1.0dev" - ] + "url": ["https://github.com/nf-core/drugresponseeval", "https://nf-co.re/drugresponseeval/dev/"], + "version": ["1.0dev"] }, { "@id": "https://w3id.org/workflowhub/workflow-ro-crate#nextflow", @@ -183,11 +170,11 @@ "version": "!>=24.04.2" }, { - "@id": "#ac53992c-1e82-45a6-9090-78a775a22a67", + "@id": "#859e0da7-cdd6-48e5-8a21-9be134a786bc", "@type": "TestSuite", "instance": [ { - "@id": "#10a1faee-1247-4383-8941-d451f2454d87" + "@id": "#595ff5f8-6ca8-4311-910c-78950b79b68d" } ], "mainEntity": { @@ -196,7 +183,7 @@ "name": "Test suite for nf-core/drugresponseeval" }, { - "@id": "#10a1faee-1247-4383-8941-d451f2454d87", + "@id": "#595ff5f8-6ca8-4311-910c-78950b79b68d", "@type": "TestInstance", "name": "GitHub Actions workflow for testing nf-core/drugresponseeval", "resource": "repos/nf-core/drugresponseeval/actions/workflows/ci.yml", @@ -321,4 +308,4 @@ "name": "Judith Bernett" } ] -} \ No newline at end of file +}