Merge branch 'dev' into longread_only

.editorconfig

@@ -31,3 +31,7 @@ indent_size = unset
 # ignore python and markdown
 [*.{py,md}]
 indent_style = unset
+
+# ignore ro-crate metadata files
+[**/ro-crate-metadata.json]
+insert_final_newline = unset

.github/ISSUE_TEMPLATE/bug_report.yml

@@ -9,7 +9,6 @@ body:
 
         - [nf-core website: troubleshooting](https://nf-co.re/usage/troubleshooting)
         - [nf-core/mag pipeline documentation](https://nf-co.re/mag/usage)
-
   - type: textarea
     id: description
     attributes:

.github/workflows/ci.yml

@@ -51,6 +51,8 @@ jobs:
 
       - name: Check out pipeline code
         uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
+        with:
+          fetch-depth: 0
 
       - name: Set up Nextflow
         uses: nf-core/setup-nextflow@v2

.github/workflows/download_pipeline.yml

@@ -28,8 +28,23 @@ env:
   NXF_ANSI_LOG: false
 
 jobs:
+  configure:
+    runs-on: ubuntu-latest
+    outputs:
+      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
@@ -52,12 +67,6 @@ 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
-        run: |
-          echo "REPO_LOWERCASE=${GITHUB_REPOSITORY,,}" >> ${GITHUB_ENV}
-          echo "REPOTITLE_LOWERCASE=$(basename ${GITHUB_REPOSITORY,,})" >> ${GITHUB_ENV}
-          echo "REPO_BRANCH=${{ github.event.inputs.testbranch || 'dev' }}" >> ${GITHUB_ENV}
-
       - name: Make a cache directory for the container images
         run: |
           mkdir -p ./singularity_container_images
@@ -66,55 +75,59 @@ jobs:
         env:
           NXF_SINGULARITY_CACHEDIR: ./singularity_container_images
         run: |
-          nf-core pipelines download ${{ env.REPO_LOWERCASE }} \
-          --revision ${{ env.REPO_BRANCH }} \
-          --outdir ./${{ env.REPOTITLE_LOWERCASE }} \
+          nf-core pipelines download ${{ needs.configure.outputs.REPO_LOWERCASE }} \
+          --revision ${{ needs.configure.outputs.REPO_BRANCH }} \
+          --outdir ./${{ needs.configure.outputs.REPOTITLE_LOWERCASE }} \
           --compress "none" \
           --container-system 'singularity' \
           --container-library "quay.io" -l "docker.io" -l "community.wave.seqera.io/library/" \
           --container-cache-utilisation 'amend' \
           --download-configuration 'yes'
 
       - name: Inspect download
-        run: tree ./${{ env.REPOTITLE_LOWERCASE }}
+        run: tree ./${{ 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: |
           image_count=$(ls -1 ./singularity_container_images | wc -l | xargs)
           echo "Initial container image count: $image_count"
-          echo "IMAGE_COUNT_INITIAL=$image_count" >> ${GITHUB_ENV}
+          echo "IMAGE_COUNT_INITIAL=$image_count" >> "$GITHUB_OUTPUT"
 
       - name: Run the downloaded pipeline (stub)
         id: stub_run_pipeline
         continue-on-error: true
         env:
           NXF_SINGULARITY_CACHEDIR: ./singularity_container_images
           NXF_SINGULARITY_HOME_MOUNT: true
-        run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -stub -profile test,singularity --outdir ./results
+        run: nextflow run ./${{needs.configure.outputs.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ needs.configure.outputs.REPO_BRANCH }}) -stub -profile test,singularity --outdir ./results
       - name: Run the downloaded pipeline (stub run not supported)
         id: run_pipeline
-        if: ${{ job.steps.stub_run_pipeline.status == failure() }}
+        if: ${{ steps.stub_run_pipeline.outcome == 'failure' }}
         env:
           NXF_SINGULARITY_CACHEDIR: ./singularity_container_images
           NXF_SINGULARITY_HOME_MOUNT: true
-        run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -profile test,singularity --outdir ./results
+        run: nextflow run ./${{ needs.configure.outputs.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ needs.configure.outputs.REPO_BRANCH }}) -profile test,singularity --outdir ./results
 
       - name: Count the downloaded number of container images
         id: count_afterwards
         run: |
           image_count=$(ls -1 ./singularity_container_images | wc -l | xargs)
           echo "Post-pipeline run container image count: $image_count"
-          echo "IMAGE_COUNT_AFTER=$image_count" >> ${GITHUB_ENV}
+          echo "IMAGE_COUNT_AFTER=$image_count" >> "$GITHUB_OUTPUT"
 
       - name: Compare container image counts
         run: |
-          if [ "${{ env.IMAGE_COUNT_INITIAL }}" -ne "${{ env.IMAGE_COUNT_AFTER }}" ]; then
-            initial_count=${{ env.IMAGE_COUNT_INITIAL }}
-            final_count=${{ env.IMAGE_COUNT_AFTER }}
+          if [ "${{ steps.count_initial.outputs.IMAGE_COUNT_INITIAL }}" -ne "${{ steps.count_afterwards.outputs.IMAGE_COUNT_AFTER }}" ]; then
+            initial_count=${{ steps.count_initial.outputs.IMAGE_COUNT_INITIAL }}
+            final_count=${{ 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!"

.nf-core.yml

@@ -5,7 +5,7 @@ lint:
     - config_defaults:
         - params.phix_reference
         - params.lambda_reference
-nf_core_version: 3.1.0
+nf_core_version: 3.1.2
 repository_type: pipeline
 template:
   author: "Hadrien Gourlé, Daniel Straub, Sabrina Krakau, James A. Fellows Yates,

.prettierignore

@@ -10,3 +10,4 @@ testing/
 testing*
 *.pyc
 bin/
+ro-crate-metadata.json

CHANGELOG.md

@@ -3,17 +3,23 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## dev [unreleased]
+## v3.3.1dev - [unreleased]
 
 ### `Added`
 
 ### `Changed`
 
+- [#731](https://github.com/nf-core/mag/pull/747) - Updated to nf-core 3.1.2 `TEMPLATE` (by @jfy133)
+
 ### `Fixed`
 
-### `Dependencies`
+- [#748](https://github.com/nf-core/mag/pull/748) - Fix broken phix reference channel when skipping phix removal (reported by @amizeranschi, fix by @muabnezor)
+- [#752](https://github.com/nf-core/mag/pull/752) - Fix QUAST results not being displayed when skipping certain steps (reported by @amizeranschi, fix by @jfy133)
+- [#753](https://github.com/nf-core/mag/pull/753) - Fix iGenomes reference support for host removal reference genome (reported by @Thomieh73, fix by @jfy133)
 
-### `Dependencies`
+### `Deprecated`
+
+### `Deprecated`
 
 ## 3.3.0 [2024-12-19]
 

LICENSE

@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) Hadrien Gourlé, Daniel Straub, Sabrina Krakau, James A. Fellows Yates, Maxime Borry
+Copyright (c) The nf-core/mag team
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

README.md

@@ -7,7 +7,8 @@
 
 [![GitHub Actions CI Status](https://github.com/nf-core/mag/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-core/mag/actions/workflows/ci.yml)
 [![GitHub Actions Linting Status](https://github.com/nf-core/mag/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/mag/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/mag/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.3589527-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.3589527)
-[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)[![Cite Publication](https://img.shields.io/badge/Cite%20Us!-Cite%20Publication-orange)](https://doi.org/10.1093/nargab/lqac007)
+[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)
+[![Cite Publication](https://img.shields.io/badge/Cite%20Us!-Cite%20Publication-orange)](https://doi.org/10.1093/nargab/lqac007)
 
 [![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A524.04.2-23aa62.svg)](https://www.nextflow.io/)
 [![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)
@@ -27,6 +28,11 @@
 
 ## Pipeline summary
 
+## 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.
+
 By default, the pipeline currently performs the following: it supports both short and long reads, quality trims the reads and adapters with [fastp](https://github.com/OpenGene/fastp) and [Porechop](https://github.com/rrwick/Porechop), and performs basic QC with [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/), and merge multiple sequencing runs.
 
 The pipeline then:

assets/multiqc_config.yml

@@ -1,8 +1,7 @@
 report_comment: >
-  This report has been generated by the <a href="https://github.com/nf-core/mag/tree/dev"
-  target="_blank">nf-core/mag</a> analysis pipeline. For information about how to
-  interpret these results, please see the <a href="https://nf-co.re/mag/dev/docs/output"
-  target="_blank">documentation</a>.
+  This report has been generated by the <a href="https://github.com/nf-core/mag/tree/dev" target="_blank">nf-core/mag</a>
+  analysis pipeline. For information about how to interpret these results, please see the
+  <a href="https://nf-co.re/mag/dev/docs/output" target="_blank">documentation</a>.
 report_section_order:
   "nf-core-mag-methods-description":
     order: -1000
@@ -19,7 +18,7 @@ data_format: "yaml"
 run_modules:
   - fastqc
   - fastp
-  - adapterRemoval
+  - adapterremoval
   - custom_content
   - bowtie2
   - busco
@@ -36,7 +35,7 @@ top_modules:
       path_filters_exclude:
         - "*trimmed*"
   - "fastp"
-  - "adapterRemoval"
+  - "adapterremoval"
   - "porechop"
   - "filtlong"
   - "fastqc":
@@ -119,12 +118,12 @@ custom_data:
 sp:
   host_removal:
     fn: "host_removal_metrics.tsv"
-  adapterRemoval:
+  adapterremoval:
     fn: "*_ar2.settings"
   kraken:
     fn_re: ".*[kraken2|centrifuge].*report.txt"
   quast:
-    fn_re: "report.*.tsv"
+    fn: "report*.tsv"
   filtlong:
     num_lines: 20
     fn_re: ".*_filtlong.log"