preprocessing v3.0.1

.github/workflows/branch.yml

@@ -21,7 +21,7 @@ jobs:
       # NOTE - this doesn't currently work if the PR is coming from a fork, due to limitations in GitHub actions secrets
       - name: Post PR comment
         if: failure()
-        uses: mshick/add-pr-comment@b8f338c590a895d50bcbfa6c5859251edc8952fc # v2
+        uses: mshick/add-pr-comment@8e4927817251f1ff60c001f04568532b38e0b4a0 # v3
         with:
           message: |
             ## This PR is against the `${{github.event.pull_request.base.ref}}` branch :x:

.github/workflows/linting.yml

@@ -11,54 +11,50 @@ jobs:
   pre-commit:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
+      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6
 
-      - name: Set up Python 3.14
-        uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6
-        with:
-          python-version: "3.14"
-
-      - name: Install pre-commit
-        run: pip install pre-commit
+      - name: Install Nextflow
+        uses: nf-core/setup-nextflow@b4ec1bc7c16a94435159de94a05253542fddf6ef # v3
 
-      - name: Run pre-commit
-        run: pre-commit run --all-files
+      - name: Run prek
+        uses: j178/prek-action@6ad80277337ad479fe43bd70701c3f7f8aa74db3 # v2
 
   nf-core:
     runs-on: ubuntu-latest
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
+        uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6
 
       - name: Install Nextflow
-        uses: nf-core/setup-nextflow@v2
+        uses: nf-core/setup-nextflow@b4ec1bc7c16a94435159de94a05253542fddf6ef # v3
 
-      - uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6
+      - uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6
         with:
           python-version: "3.14"
           architecture: "x64"
 
+      - name: Setup uv
+        uses: astral-sh/setup-uv@08807647e7069bb48b6ef5acd8ec9567f424441b # v8.1.0
+
       - name: read .nf-core.yml
         uses: pietrobolcato/action-read-yaml@9f13718d61111b69f30ab4ac683e67a56d254e1d # 1.1.0
         id: read_yml
         with:
           config: ${{ github.workspace }}/.nf-core.yml
 
       - name: Install dependencies
-        run: |
-          python -m pip install --upgrade pip
-          pip install nf-core==${{ steps.read_yml.outputs['nf_core_version'] }}
+        run: uv tool install nf-core==${{ steps.read_yml.outputs['nf_core_version'] }}
 
       - name: Run nf-core pipelines lint
-        if: ${{ github.base_ref != 'master' }}
+        if: ${{ github.base_ref != 'master' || github.base_ref != 'main' }}
         env:
           GITHUB_COMMENTS_URL: ${{ github.event.pull_request.comments_url }}
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           GITHUB_PR_COMMIT: ${{ github.event.pull_request.head.sha }}
         run: nf-core -l lint_log.txt pipelines lint --dir ${GITHUB_WORKSPACE} --markdown lint_results.md
 
       - name: Run nf-core pipelines lint --release
-        if: ${{ github.base_ref == 'master' }}
+        if: ${{ github.base_ref == 'master' || github.base_ref == 'main' }}
         env:
           GITHUB_COMMENTS_URL: ${{ github.event.pull_request.comments_url }}
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
@@ -71,7 +67,7 @@ jobs:
 
       - name: Upload linting log file artifact
         if: ${{ always() }}
-        uses: actions/upload-artifact@330a01c490aca151604b8cf639adc76d48f6c5d4 # v5
+        uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7
         with:
           name: linting-logs
           path: |

.github/workflows/linting_comment.yml

@@ -11,7 +11,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Download lint results
-        uses: dawidd6/action-download-artifact@ac66b43f0e6a346234dd65d4d0c8fbb31cb316e5 # v11
+        uses: dawidd6/action-download-artifact@b6e2e70617bc3265edd6dab6c906732b2f1ae151 # v21
         with:
           workflow: linting.yml
           workflow_conclusion: completed
@@ -21,7 +21,7 @@ jobs:
         run: echo "pr_number=$(cat linting-logs/PR_number.txt)" >> $GITHUB_OUTPUT
 
       - name: Post PR comment
-        uses: marocchino/sticky-pull-request-comment@773744901bac0e8cbb5a0dc842800d45e9b2b405 # v2
+        uses: marocchino/sticky-pull-request-comment@70d2764d1a7d5d9560b100cbea0077fc8f633987 # v3
         with:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           number: ${{ steps.pr_number.outputs.pr_number }}

.github/workflows/nf-test.yml

@@ -18,7 +18,7 @@ concurrency:
 
 env:
   GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-  NFT_VER: "0.9.3"
+  NFT_VER: "0.9.5"
   NFT_WORKDIR: "~"
   NXF_ANSI_LOG: false
   NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity
@@ -76,7 +76,7 @@ jobs:
           - isMain: false
             profile: "singularity"
         NXF_VER:
-          - 25.10.0
+          - 26.04.0
           - latest-everything
     env:
       NXF_ANSI_LOG: false

.gitignore

@@ -9,3 +9,7 @@ testing*
 null/
 .nf-test*
 test_fc
+.lineage/
+# pixi environments
+.pixi/*
+!.pixi/config.toml

.nf-core.yml

@@ -1,30 +1,34 @@
 lint:
   files_exist:
-    - CODE_OF_CONDUCT.md
-    - CITATIONS.md
-    - assets/nf-core-preprocessing_logo_light.png
-    - docs/images/nf-core-preprocessing_logo_light.png
-    - docs/images/nf-core-preprocessing_logo_dark.png
     - .github/ISSUE_TEMPLATE/config.yml
-    - .github/workflows/awstest.yml
     - .github/workflows/awsfulltest.yml
-  files_unchanged:
+    - .github/workflows/awstest.yml
+    - CITATIONS.md
     - CODE_OF_CONDUCT.md
     - assets/nf-core-preprocessing_logo_light.png
-    - docs/images/nf-core-preprocessing_logo_light.png
+    - docs/CONTRIBUTING.md
     - docs/images/nf-core-preprocessing_logo_dark.png
+    - docs/images/nf-core-preprocessing_logo_light.png
+  files_unchanged:
     - .github/ISSUE_TEMPLATE/bug_report.yml
     - .github/PULL_REQUEST_TEMPLATE.md
-    - docs/README.md
+    - .gitignore
+    - CODE_OF_CONDUCT.md
     - LICENSE
+    - assets/nf-core-preprocessing_logo_light.png
+    - docs/README.md
+    - docs/images/nf-core-preprocessing_logo_dark.png
+    - docs/images/nf-core-preprocessing_logo_light.png
   merge_markers:
     - bin/cmgg_genelists
+    - .pixi/envs
   multiqc_config: false
   nextflow_config: false
+  schema_params: false # TMP
   template_strings:
     - bin/cmgg_genelists
   nf_test_content: false
-nf_core_version: 3.5.2
+nf_core_version: 4.0.2
 repository_type: pipeline
 template:
   author: Matthias De Smet, Nicolas Vannieuwkerke
@@ -35,4 +39,4 @@ template:
   org: nf-cmgg
   outdir: .
   skip_features: ["fastqc"]
-  version: 3.0.0
+  version: 3.0.1

.prettierignore

@@ -1,6 +1,4 @@
 email_template.html
-adaptivecard.json
-slackreport.json
 .nextflow*
 work/
 data/

.vscode/settings.json

@@ -1,3 +1,4 @@
 {
-    "markdown.styles": ["public/vscode_markdown.css"]
+    "markdown.styles": ["public/vscode_markdown.css"],
+    "nextflow.telemetry.enabled": false
 }

CHANGELOG.md

@@ -3,6 +3,16 @@
 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).
 
+## 3.0.1dev
+
+- Add parameter typing to make strict syntax runs work more properly
+- Bumped minimal Nextflow version to 26.04.0 to allow for strict syntax and other improvements
+- Fix an issue with `mosdepth` environment variables not being correctly set on GCP
+- Bump `mosdepth` module to 0.3.14
+- Bump nf-core template to v4.0.2
+- Fix fastq outputs when aligner is set to `false` or unsupported genome, which were not being correctly emitted in the previous version
+- Fix `FALCO` module not being correctly run on fastq samples, which was caused by an issue with the branching logic in the previous version
+
 ## 3.0.0
 
 - Add `MultiQC-SAV` module for Illumina Run QC reports

README.md

@@ -5,7 +5,7 @@
 [![GitHub Actions Linting Status](https://github.com/nf-cmgg/preprocessing/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-cmgg/preprocessing/actions/workflows/linting.yml)[![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)
 
-[![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.10.0-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)
+[![Nextflow](https://img.shields.io/badge/version-%E2%89%A526.04.0-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)
 [![nf-core template version](https://img.shields.io/badge/nf--core_template-3.5.1-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.5.1)
 [![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)
 [![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)
@@ -59,6 +59,16 @@ nextflow run nf-cmgg/preprocessing \
 > 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/usage/configuration#custom-configuration-files).
 
+## Development environment
+
+A [pixi](https://pixi.prefix.dev/latest/) development environment is available for this pipeline. Run the following command to install the environment:
+
+```
+pixi install
+```
+
+Then run `pixi shell` to enter the environment and start developing.
+
 ## Credits
 
 nf-cmgg/preprocessing was originally written by the CMGG ICT team.

assets/multiqc_config.yml

@@ -1,5 +1,5 @@
 report_comment: >
-  This report has been generated by the <a href="https://github.com/nf-cmgg/preprocessing/releases/tag/3.0.0" target="_blank">nf-cmgg/preprocessing</a> analysis pipeline.
+  This report has been generated by the <a href="https://github.com/nf-cmgg/preprocessing/releases/tag/3.0.1" target="_blank">nf-cmgg/preprocessing</a> analysis pipeline.
 report_section_order:
   "nf-cmgg-preprocessing-methods-description":
     order: -1000

assets/schema_input.json

@@ -28,10 +28,10 @@
             "genome": {
                 "meta": ["genome"],
                 "type": "string",
-                "description": "Genome build. Currently supported genomes include GRCh38, GRCm39 and GRCz11",
+                "description": "Genome build. Currently supported genomes include GRCh38, GRCh38-noalt, GRCm39, GRCz11, hg38 and hg38-noalt",
                 "pattern": "^[a-zA-Z0-9_-]+$",
                 "default": null,
-                "enum": ["GRCh38", "GRCm39", "GRCz11", "hg38", "hg38-noalt"]
+                "enum": ["GRCh38", "GRCh38-noalt", "GRCm39", "GRCz11", "hg38", "hg38-noalt"]
             },
             "aligner": {
                 "meta": ["aligner"],

assets/schema_sampleinfo.json

@@ -47,10 +47,10 @@
             "genome": {
                 "meta": ["genome"],
                 "type": "string",
-                "description": "Genome build. Currently supported genomes include GRCh38, GRCm39 and GRCz11",
+                "description": "Genome build. Currently supported genomes include GRCh38, GRCh38-noalt, GRCm39, GRCz11, hg38 and hg38-noalt",
                 "pattern": "^[a-zA-Z0-9_-]+$",
                 "default": null,
-                "enum": ["GRCh38", "GRCm39", "GRCz11", "hg38", "hg38-noalt"]
+                "enum": ["GRCh38", "GRCh38-noalt", "GRCm39", "GRCz11", "hg38", "hg38-noalt"]
             },
             "vivar_project": {
                 "meta": ["vivar_project"],

conf/base.config

@@ -15,7 +15,7 @@ process {
     time          = { 4.h * task.attempt }
     errorStrategy = { task.exitStatus in ((130..145) + 104 + 175 + 50001 + 50002 + 50003 + 50004 + 50005 + 50006) ? 'retry' : 'finish' }
     maxRetries    = 3
-    maxErrors     = '-1'
+    maxErrors     = -1
 
     // Process-specific resource requirements
     withLabel: process_single {

conf/containers_conda_lock_files_amd64.config

@@ -0,0 +1,2 @@
+process { withName: 'MULTIQC' { container = 'modules/nf-core/multiqc/.conda-lock/linux_amd64-bd-db7c73dae76bc9e6_1.txt' } }
+process { withName: 'MULTIQCSAV' { container = 'modules/nf-core/multiqcsav/.conda-lock/linux_amd64-bd-644a84cef31cc4aa_1.txt' } }

conf/containers_conda_lock_files_arm64.config

@@ -0,0 +1,2 @@
+process { withName: 'MULTIQC' { container = 'modules/nf-core/multiqc/.conda-lock/linux_arm64-bd-d167b8012595a136_1.txt' } }
+process { withName: 'MULTIQCSAV' { container = 'modules/nf-core/multiqcsav/.conda-lock/linux_arm64-bd-039d1ec6b47ba325_1.txt' } }

conf/containers_docker_amd64.config

@@ -0,0 +1,2 @@
+process { withName: 'MULTIQC' { container = 'community.wave.seqera.io/library/multiqc:1.34--db7c73dae76bc9e6' } }
+process { withName: 'MULTIQCSAV' { container = 'community.wave.seqera.io/library/multiqc_multiqc_sav_pip_interop:644a84cef31cc4aa' } }

conf/containers_docker_arm64.config

@@ -0,0 +1,2 @@
+process { withName: 'MULTIQC' { container = 'community.wave.seqera.io/library/multiqc:1.34--d167b8012595a136' } }
+process { withName: 'MULTIQCSAV' { container = 'community.wave.seqera.io/library/multiqc_multiqc_sav_pip_interop:039d1ec6b47ba325' } }

conf/containers_singularity_https_amd64.config

@@ -0,0 +1,2 @@
+process { withName: 'MULTIQC' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/1b/1bef8af6be88c5733461959c46ac8ef73d18f65277f62a1695d0e1633054f9c2/data' } }
+process { withName: 'MULTIQCSAV' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/45/4590c19f294469392d1bd2689eb9d4a06f18d20f64c5dbc0bbc17473c9941b4e/data' } }

conf/containers_singularity_https_arm64.config

@@ -0,0 +1,2 @@
+process { withName: 'MULTIQC' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/9a/9a1fec9662a152683e6fcae440d0ce20920b3b89dc62d1e3a52e73f92eba0969/data' } }
+process { withName: 'MULTIQCSAV' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b0/b047611068a4009d62d8352e8bb4ab27fa993708a82c029f115e6758b2e44bec/data' } }

conf/containers_singularity_oras_amd64.config

@@ -0,0 +1,2 @@
+process { withName: 'MULTIQC' { container = 'oras://community.wave.seqera.io/library/multiqc:1.34--4fc8657c816047c0' } }
+process { withName: 'MULTIQCSAV' { container = 'oras://community.wave.seqera.io/library/multiqc_multiqc_sav_pip_interop:9ebe780f2738c655' } }

conf/containers_singularity_oras_arm64.config

@@ -0,0 +1,2 @@
+process { withName: 'MULTIQC' { container = 'oras://community.wave.seqera.io/library/multiqc:1.34--7fbd82d945c06726' } }
+process { withName: 'MULTIQCSAV' { container = 'oras://community.wave.seqera.io/library/multiqc_multiqc_sav_pip_interop:fc57bb53140baade' } }