nf-core · Felix-Kummer · Mar 6, 2025 · Jan 20, 2025 · Jan 27, 2025 · Mar 5, 2025
diff --git 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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -7,7 +7,7 @@ repos:
           - [email protected]
 
   - 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
@@ -3,7 +3,9 @@
     <source media="(prefers-color-scheme: dark)" srcset="docs/images/nf-core-rangeland_logo_dark.png">
     <img alt="nf-core/rangeland" src="docs/images/nf-core-rangeland_logo_light.png">
   </picture>
-</h1>[![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)
+</h1>
+
+[![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
@@ -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 '${workflow}' object
 data: |
   <h4>Methods</h4>
   <p>Data was processed using nf-core/rangeland v${workflow.manifest.version} ${doi_text} of the nf-core collection of workflows (<a href="https://doi.org/10.1038/s41587-020-0439-x">Ewels <em>et al.</em>, 2020</a>), utilising reproducible software environments from the Bioconda (<a href="https://doi.org/10.1038/s41592-018-0046-7">Grüning <em>et al.</em>, 2018</a>) and Biocontainers (<a href="https://doi.org/10.1093/bioinformatics/btx192">da Veiga Leprevost <em>et al.</em>, 2017</a>) projects.</p>

diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml
@@ -1,8 +1,7 @@
 report_comment: >
-  This report has been generated by the <a href="https://github.com/nf-core/rangeland/tree/dev"
-  target="_blank">nf-core/rangeland</a> analysis pipeline. For information about how
-  to interpret these results, please see the <a href="https://nf-co.re/rangeland/dev/docs/output"
-  target="_blank">documentation</a>.
+  This report has been generated by the <a href="https://github.com/nf-core/rangeland/tree/dev" target="_blank">nf-core/rangeland</a>
+  analysis pipeline. For information about how to interpret these results, please see the
+  <a href="https://nf-co.re/rangeland/dev/docs/output" target="_blank">documentation</a>.
 report_section_order:
   "nf-core-rangeland-methods-description":
     order: -1000

diff --git 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
diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf
diff --git a/modules/nf-core/multiqc/tests/main.nf.test.snap b/modules/nf-core/multiqc/tests/main.nf.test.snap
diff --git 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
@@ -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"
         }
     ]
-}
+}
diff --git a/subworkflows/local/higher_level.nf → subworkflows/local/higher_level/main.nf b/subworkflows/local/higher_level.nf → 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 → subworkflows/local/preprocessing/main.nf b/subworkflows/local/preprocessing.nf → 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
@@ -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'
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~