diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index fd1e83a..0abeb39 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 d4a9b40..99a975e 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -2,7 +2,7 @@ lint: files_exist: - conf/igenomes.config - conf/igenomes_ignored.config -nf_core_version: 3.1.1 +nf_core_version: 3.2.0 repository_type: pipeline template: author: Fabian Lehmann, David Frantz, Felix Kummer 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 b884b8d..1fd28ed 100644 --- a/README.md +++ b/README.md @@ -3,7 +3,9 @@ nf-core/rangeland -[![GitHub Actions CI Status](https://github.com/nf-core/rangeland/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-core/rangeland/actions/workflows/ci.yml) + + +[![GitHub Actions CI Status](https://github.com/nf-core/rangeland/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-core/rangeland/actions/workflows/ci.yml) [![GitHub Actions Linting Status](https://github.com/nf-core/rangeland/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/rangeland/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/rangeland/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.14679189-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.14679189) [![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com) diff --git a/assets/methods_description_template.yml b/assets/methods_description_template.yml index ae33245..c9b9cc5 100644 --- a/assets/methods_description_template.yml +++ b/assets/methods_description_template.yml @@ -3,8 +3,6 @@ description: "Suggested text and references to use when describing pipeline usag section_name: "nf-core/rangeland Methods Description" section_href: "https://github.com/nf-core/rangeland" plot_type: "html" -## TODO nf-core: Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline -## You inject any metadata in the Nextflow '${workflow}' object data: |

Methods

Data was processed using nf-core/rangeland v${workflow.manifest.version} ${doi_text} of the nf-core collection of workflows (Ewels et al., 2020), utilising reproducible software environments from the Bioconda (Grüning et al., 2018) and Biocontainers (da Veiga Leprevost et al., 2017) projects.

diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index 8840532..d2ae102 100644 --- a/assets/multiqc_config.yml +++ b/assets/multiqc_config.yml @@ -1,8 +1,7 @@ report_comment: > - This report has been generated by the nf-core/rangeland analysis pipeline. For information about how - to interpret these results, please see the documentation. + This report has been generated by the nf-core/rangeland + analysis pipeline. For information about how to interpret these results, please see the + documentation. report_section_order: "nf-core-rangeland-methods-description": order: -1000 diff --git a/modules.json b/modules.json index f794519..1c16202 100644 --- a/modules.json +++ b/modules.json @@ -7,7 +7,7 @@ "nf-core": { "multiqc": { "branch": "master", - "git_sha": "cf17ca47590cc578dfb47db1c2a44ef86f89976d", + "git_sha": "81880787133db07d9b4c1febd152c090eb8325dc", "installed_by": ["modules"] }, "untar": { diff --git a/modules/nf-core/multiqc/environment.yml b/modules/nf-core/multiqc/environment.yml index 6f5b867..a27122c 100644 --- a/modules/nf-core/multiqc/environment.yml +++ b/modules/nf-core/multiqc/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::multiqc=1.25.1 + - bioconda::multiqc=1.27 diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf index cc0643e..58d9313 100644 --- a/modules/nf-core/multiqc/main.nf +++ b/modules/nf-core/multiqc/main.nf @@ -3,8 +3,8 @@ process MULTIQC { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/multiqc:1.25.1--pyhdfd78af_0' : - 'biocontainers/multiqc:1.25.1--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/multiqc:1.27--pyhdfd78af_0' : + 'biocontainers/multiqc:1.27--pyhdfd78af_0' }" input: path multiqc_files, stageAs: "?/*" diff --git a/modules/nf-core/multiqc/tests/main.nf.test.snap b/modules/nf-core/multiqc/tests/main.nf.test.snap index 2fcbb5f..7b7c132 100644 --- a/modules/nf-core/multiqc/tests/main.nf.test.snap +++ b/modules/nf-core/multiqc/tests/main.nf.test.snap @@ -2,14 +2,14 @@ "multiqc_versions_single": { "content": [ [ - "versions.yml:md5,41f391dcedce7f93ca188f3a3ffa0916" + "versions.yml:md5,8f3b8c1cec5388cf2708be948c9fa42f" ] ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.2", + "nextflow": "24.10.4" }, - "timestamp": "2024-10-02T17:51:46.317523" + "timestamp": "2025-01-27T09:29:57.631982377" }, "multiqc_stub": { "content": [ @@ -17,25 +17,25 @@ "multiqc_report.html", "multiqc_data", "multiqc_plots", - "versions.yml:md5,41f391dcedce7f93ca188f3a3ffa0916" + "versions.yml:md5,8f3b8c1cec5388cf2708be948c9fa42f" ] ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.2", + "nextflow": "24.10.4" }, - "timestamp": "2024-10-02T17:52:20.680978" + "timestamp": "2025-01-27T09:30:34.743726958" }, "multiqc_versions_config": { "content": [ [ - "versions.yml:md5,41f391dcedce7f93ca188f3a3ffa0916" + "versions.yml:md5,8f3b8c1cec5388cf2708be948c9fa42f" ] ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.2", + "nextflow": "24.10.4" }, - "timestamp": "2024-10-02T17:52:09.185842" + "timestamp": "2025-01-27T09:30:21.44383553" } } \ No newline at end of file diff --git a/nextflow.config b/nextflow.config index 9df08cf..006fe71 100644 --- a/nextflow.config +++ b/nextflow.config @@ -214,14 +214,14 @@ 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 @@ -283,7 +283,7 @@ 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 694b4ff..71ddf8b 100644 --- a/ro-crate-metadata.json +++ b/ro-crate-metadata.json @@ -127,11 +127,7 @@ }, { "@id": "main.nf", - "@type": [ - "File", - "SoftwareSourceCode", - "ComputationalWorkflow" - ], + "@type": ["File", "SoftwareSourceCode", "ComputationalWorkflow"], "creator": [ { "@id": "https://orcid.org/0009-0007-1154-6980" @@ -150,30 +146,21 @@ "trend-analysis", "trends" ], - "license": [ - "MIT" - ], + "license": ["MIT"], "maintainer": [ { "@id": "https://orcid.org/0009-0007-1154-6980" } ], - "name": [ - "nf-core/rangeland" - ], + "name": ["nf-core/rangeland"], "programmingLanguage": { "@id": "https://w3id.org/workflowhub/workflow-ro-crate#nextflow" }, "sdPublisher": { "@id": "https://nf-co.re/" }, - "url": [ - "https://github.com/nf-core/rangeland", - "https://nf-co.re/rangeland/dev/" - ], - "version": [ - "1.1.0dev" - ] + "url": ["https://github.com/nf-core/rangeland", "https://nf-co.re/rangeland/dev/"], + "version": ["1.1.0dev"] }, { "@id": "https://w3id.org/workflowhub/workflow-ro-crate#nextflow", @@ -346,4 +333,4 @@ "name": "Felix Kummer" } ] -} \ No newline at end of file +} diff --git a/subworkflows/local/higher_level.nf b/subworkflows/local/higher_level/main.nf similarity index 84% rename from subworkflows/local/higher_level.nf rename to subworkflows/local/higher_level/main.nf index 9c9fe43..2dbc711 100644 --- a/subworkflows/local/higher_level.nf +++ b/subworkflows/local/higher_level/main.nf @@ -1,7 +1,7 @@ -include { HIGHER_LEVEL_CONFIG } from '../../modules/local/higher_level_force_config/main' -include { FORCE_HIGHER_LEVEL } from '../../modules/local/force-higher_level/main' -include { FORCE_MOSAIC } from '../../modules/local/force-mosaic/main' -include { FORCE_PYRAMID } from '../../modules/local/force-pyramid/main' +include { HIGHER_LEVEL_CONFIG } from '../../../modules/local/higher_level_force_config/main' +include { FORCE_HIGHER_LEVEL } from '../../../modules/local/force-higher_level/main' +include { FORCE_MOSAIC } from '../../../modules/local/force-mosaic/main' +include { FORCE_PYRAMID } from '../../../modules/local/force-pyramid/main' workflow HIGHER_LEVEL { diff --git a/subworkflows/local/preprocessing.nf b/subworkflows/local/preprocessing/main.nf similarity index 86% rename from subworkflows/local/preprocessing.nf rename to subworkflows/local/preprocessing/main.nf index 8690157..ae6f5dc 100644 --- a/subworkflows/local/preprocessing.nf +++ b/subworkflows/local/preprocessing/main.nf @@ -1,8 +1,8 @@ -include { FORCE_GENERATE_TILE_ALLOW_LIST } from '../../modules/local/force-generate_tile_allow_list/main' -include { FORCE_GENERATE_ANALYSIS_MASK } from '../../modules/local/force-generate_analysis_mask/main' -include { PREPROCESS_CONFIG } from '../../modules/local/preprocess_force_config/main' -include { FORCE_PREPROCESS } from '../../modules/local/force-preprocess/main' -include { MERGE as MERGE_BOA; MERGE as MERGE_QAI } from '../../modules/local/merge/main' +include { FORCE_GENERATE_TILE_ALLOW_LIST } from '../../../modules/local/force-generate_tile_allow_list/main' +include { FORCE_GENERATE_ANALYSIS_MASK } from '../../../modules/local/force-generate_analysis_mask/main' +include { PREPROCESS_CONFIG } from '../../../modules/local/preprocess_force_config/main' +include { FORCE_PREPROCESS } from '../../../modules/local/force-preprocess/main' +include { MERGE as MERGE_BOA; MERGE as MERGE_QAI } from '../../../modules/local/merge/main' workflow PREPROCESSING { diff --git a/workflows/rangeland.nf b/workflows/rangeland.nf index 8cc12a1..d776d08 100644 --- a/workflows/rangeland.nf +++ b/workflows/rangeland.nf @@ -19,8 +19,8 @@ include { methodsDescriptionText } from '../subworkflows/local/utils_nfcore_rang // // SUBWORKFLOW: Consisting of a mix of local and nf-core/modules // -include { PREPROCESSING } from '../subworkflows/local/preprocessing' -include { HIGHER_LEVEL } from '../subworkflows/local/higher_level' +include { PREPROCESSING } from '../subworkflows/local/preprocessing/main' +include { HIGHER_LEVEL } from '../subworkflows/local/higher_level/main' /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~