Make the pipeline a typed pipeline that can be included in another pipeline

.github/PULL_REQUEST_TEMPLATE.md

@@ -18,8 +18,8 @@ Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/diff
 - [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/differentialabundance/tree/master/docs/CONTRIBUTING.md)
 - [ ] If necessary, also make a PR on the nf-core/differentialabundance _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository.
 - [ ] Make sure your code lints (`nf-core pipelines lint`).
-- [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --outdir <OUTDIR>`).
-- [ ] Check for unexpected warnings in debug mode (`nextflow run . -profile debug,test,docker --outdir <OUTDIR>`).
+- [ ] Ensure the test suite passes (`nextflow run . -profile test,docker -output-dir <OUTDIR>`).
+- [ ] Check for unexpected warnings in debug mode (`nextflow run . -profile debug,test,docker -output-dir <OUTDIR>`).
 - [ ] Usage Documentation in `docs/usage.md` is updated.
 - [ ] Output Documentation in `docs/output.md` is updated.
 - [ ] `CHANGELOG.md` is updated.

.github/actions/build-nextflow/action.yml

@@ -0,0 +1,35 @@
+name: "Build Nextflow"
+description: "TEMPORARY: builds a Nextflow launcher from a pinned upstream commit and uploads it as an artifact"
+# The output {} block needs nextflow-io/nextflow#7646 and #7674, and including rnaseq in another
+# pipeline needs #7213. These are merged upstream but not in a release yet. Delete this action, the
+# build-nextflow jobs and the custom-install steps in .github/actions/nf-test/action.yml once a
+# release contains them.
+runs:
+  using: "composite"
+  steps:
+    - name: Check out Nextflow
+      uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7
+      with:
+        repository: nextflow-io/nextflow
+        ref: 5272797c4e9b114c94e93a01e540b13c08b6c5a9
+        path: nextflow-src
+
+    - name: Set up Java
+      uses: actions/setup-java@de7274f081f381c8f8158605e0321c36c376e2e6 # v6.0.1
+      with:
+        distribution: temurin
+        java-version: "21"
+
+    - name: Build launcher
+      shell: bash
+      working-directory: nextflow-src
+      run: |
+        make pack
+        cp build/releases/nextflow-*-dist "${{ runner.temp }}/nextflow"
+
+    - name: Upload launcher
+      uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7
+      with:
+        name: nextflow-custom
+        path: ${{ runner.temp }}/nextflow
+        retention-days: 1

.github/actions/nf-test/action.yml

@@ -19,11 +19,38 @@ inputs:
 runs:
   using: "composite"
   steps:
+    # TEMPORARY: the typed pipeline needs nextflow-io/nextflow#7213, #7646 and #7674, which are not in a
+    # release yet. Every entry except latest-everything runs the launcher built by the
+    # build-nextflow job. Restore the plain setup-nextflow step once a release contains them.
     - name: Setup Nextflow
+      if: env.NXF_VERSION == 'latest-everything'
       uses: nf-core/setup-nextflow@b4ec1bc7c16a94435159de94a05253542fddf6ef # v3
       with:
         version: "${{ env.NXF_VERSION }}"
 
+    - name: Set up Java for custom Nextflow
+      if: env.NXF_VERSION != 'latest-everything'
+      uses: actions/setup-java@de7274f081f381c8f8158605e0321c36c376e2e6 # v6.0.1
+      with:
+        distribution: temurin
+        java-version: "21"
+
+    - name: Download custom Nextflow
+      if: env.NXF_VERSION != 'latest-everything'
+      uses: actions/download-artifact@3e5f45b2cfb9172054b4087a40e8e0b5a5461e7c # v8.0.1
+      with:
+        name: nextflow-custom
+        path: ${{ runner.temp }}/nextflow-custom
+
+    - name: Install custom Nextflow
+      if: env.NXF_VERSION != 'latest-everything'
+      shell: bash
+      run: |
+        mkdir -p "$HOME/.local/bin"
+        install -m 755 "${{ runner.temp }}/nextflow-custom/nextflow" "$HOME/.local/bin/nextflow"
+        echo "$HOME/.local/bin" >> "$GITHUB_PATH"
+        "$HOME/.local/bin/nextflow" -version
+
     - name: Set up Python
       uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6
       with:
@@ -60,6 +87,8 @@ runs:
       shell: bash
       env:
         NFT_WORKDIR: ${{ env.NFT_WORKDIR }}
+        # TEMPORARY: patched nf-schema (validateParameters blocks on Channel params), remove once released
+        NXF_PLUGINS_TEST_REPOSITORY: https://github.com/pinin4fjords/nf-schema/releases/download/2.7.2-channel.5/nf-schema-2.7.2-channel.5-meta.json
       run: |
         nf-test test \
           --profile=+${{ inputs.profile }} \

.github/workflows/awsfulltest.yml

@@ -53,10 +53,7 @@ jobs:
                 message = ':x: *differentialabundance/test_full* failed :crying_cat_face:'
               }
             }
-          parameters: |
-            {
-              "outdir": "s3://${{ vars.AWS_S3_BUCKET }}/differentialabundance/results-${{ steps.revision.outputs.revision }}"
-            }
+            outputDir = 's3://${{ vars.AWS_S3_BUCKET }}/differentialabundance/results-${{ steps.revision.outputs.revision }}'
           profiles: test_full
 
       - uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7

.github/workflows/awstest.yml

@@ -19,10 +19,8 @@ jobs:
           compute_env: ${{ vars.TOWER_COMPUTE_ENV }}
           revision: ${{ github.sha }}
           workdir: s3://${{ vars.AWS_S3_BUCKET }}/work/differentialabundance/work-${{ github.sha }}
-          parameters: |
-            {
-              "outdir": "s3://${{ vars.AWS_S3_BUCKET }}/differentialabundance/results-test-${{ github.sha }}"
-            }
+          nextflow_config: |
+            outputDir = 's3://${{ vars.AWS_S3_BUCKET }}/differentialabundance/results-test-${{ github.sha }}'
           profiles: test
 
       - uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7

.github/workflows/linting.yml

@@ -51,6 +51,7 @@ jobs:
           GITHUB_COMMENTS_URL: ${{ github.event.pull_request.comments_url }}
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           GITHUB_PR_COMMIT: ${{ github.event.pull_request.head.sha }}
+          NXF_PLUGINS_TEST_REPOSITORY: https://github.com/pinin4fjords/nf-schema/releases/download/2.7.2-channel.5/nf-schema-2.7.2-channel.5-meta.json
         run: nf-core -l lint_log.txt pipelines lint --dir ${GITHUB_WORKSPACE} --markdown lint_results.md
 
       - name: Run nf-core pipelines lint --release
@@ -59,6 +60,7 @@ jobs:
           GITHUB_COMMENTS_URL: ${{ github.event.pull_request.comments_url }}
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           GITHUB_PR_COMMIT: ${{ github.event.pull_request.head.sha }}
+          NXF_PLUGINS_TEST_REPOSITORY: https://github.com/pinin4fjords/nf-schema/releases/download/2.7.2-channel.5/nf-schema-2.7.2-channel.5-meta.json
         run: nf-core -l lint_log.txt pipelines lint --release --dir ${GITHUB_WORKSPACE} --markdown lint_results.md
 
       - name: Save PR number

.github/workflows/nf-test.yml

@@ -58,9 +58,20 @@ jobs:
           echo ${{ steps.set-shards.outputs.shard }}
           echo ${{ steps.set-shards.outputs.total_shards }}
 
+  # TEMPORARY: builds the Nextflow used by every nf-test job, see .github/actions/build-nextflow
+  build-nextflow:
+    name: build-nextflow
+    needs: [nf-test-changes]
+    if: ${{ needs.nf-test-changes.outputs.total_shards != '0' }}
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7
+
+      - uses: ./.github/actions/build-nextflow
+
   nf-test:
     name: "${{ matrix.profile }} | ${{ matrix.NXF_VER }} | ${{ matrix.shard }}/${{ needs.nf-test-changes.outputs.total_shards }}"
-    needs: [nf-test-changes]
+    needs: [nf-test-changes, build-nextflow]
     if: ${{ needs.nf-test-changes.outputs.total_shards != '0' }}
     runs-on: # use self-hosted runners
       - runs-on=${{ github.run_id }}-nf-test
@@ -80,7 +91,7 @@ jobs:
           - isMain: false
             profile: "singularity"
         NXF_VER:
-          - "25.10.4"
+          - "26.09.0-edge"
           - "latest-everything"
     env:
       NXF_ANSI_LOG: false

.nf-core.yml

@@ -2,17 +2,164 @@ lint:
   files_exist:
     - assets/multiqc_config.yml
   files_unchanged:
+    - .github/PULL_REQUEST_TEMPLATE.md
+    - .github/workflows/linting.yml
     - assets/nf-core-differentialabundance_logo_light.png
     - docs/images/nf-core-differentialabundance_logo_light.png
     - docs/images/nf-core-differentialabundance_logo_dark.png
   multiqc_config: false
+  # Pipeline parameters and their defaults are declared in the typed `params {}` block of main.nf,
+  # which `nextflow config` (used by the lint) does not see. Each parameter is ignored individually.
   nextflow_config:
+    - params.outdir
+    - params.input
     - config_defaults:
         - params.logo_file
         - params.css_file
         - params.citations_file
         - params.report_file
         - params.paramsheet
+        - params.affy_background
+        - params.affy_bgversion
+        - params.affy_build_annotation
+        - params.affy_destructive
+        - params.affy_file_name_col
+        - params.affy_rm_extra
+        - params.affy_rm_mask
+        - params.affy_rm_outliers
+        - params.decoupler_methods
+        - params.decoupler_min_n
+        - params.deseq2_alpha
+        - params.deseq2_alt_hypothesis
+        - params.deseq2_fit_type
+        - params.deseq2_independent_filtering
+        - params.deseq2_lfc_threshold
+        - params.deseq2_min_replicates_for_replace
+        - params.deseq2_minmu
+        - params.deseq2_p_adjust_method
+        - params.deseq2_sf_type
+        - params.deseq2_shrink_lfc
+        - params.deseq2_test
+        - params.deseq2_use_t
+        - params.deseq2_vs_blind
+        - params.deseq2_vs_method
+        - params.deseq2_vst_nsub
+        - params.differential_feature_id_column
+        - params.differential_max_pval
+        - params.differential_max_qval
+        - params.differential_method
+        - params.differential_min_fold_change
+        - params.differential_palette_name
+        - params.differential_subset_to_contrast_samples
+        - params.dream_adjust_method
+        - params.dream_apply_voom
+        - params.dream_confint
+        - params.dream_ddf
+        - params.dream_lfc
+        - params.dream_p_value
+        - params.dream_proportion
+        - params.dream_reml
+        - params.dream_robust
+        - params.dream_stdev_coef_lim
+        - params.dream_trend
+        - params.dream_winsor_tail_p
+        - params.exploratory_assay_names
+        - params.exploratory_clustering_method
+        - params.exploratory_cor_method
+        - params.exploratory_final_assay
+        - params.exploratory_log2_assays
+        - params.exploratory_mad_threshold
+        - params.exploratory_main_variable
+        - params.exploratory_n_features
+        - params.exploratory_palette_name
+        - params.exploratory_whisker_distance
+        - params.features_gtf_feature_type
+        - params.features_gtf_table_first_field
+        - params.features_id_col
+        - params.features_metadata_cols
+        - params.features_name_col
+        - params.features_type
+        - params.filtering_min_proportion_not_na
+        - params.filtering_min_samples
+        - params.functional_method
+        - params.gprofiler2_background_file
+        - params.gprofiler2_correction_method
+        - params.gprofiler2_domain_scope
+        - params.gprofiler2_evcodes
+        - params.gprofiler2_max_qval
+        - params.gprofiler2_measure_underrepresentation
+        - params.gprofiler2_min_diff
+        - params.gprofiler2_palette_name
+        - params.gprofiler2_significant
+        - params.grea_permutation
+        - params.grea_set_max
+        - params.grea_set_min
+        - params.gsea_make_sets
+        - params.gsea_median
+        - params.gsea_metric
+        - params.gsea_norm
+        - params.gsea_nperm
+        - params.gsea_num
+        - params.gsea_order
+        - params.gsea_permute
+        - params.gsea_plot_top_x
+        - params.gsea_rnd_type
+        - params.gsea_save_rnd_lists
+        - params.gsea_scoring_scheme
+        - params.gsea_set_max
+        - params.gsea_set_min
+        - params.gsea_sort
+        - params.gsea_zip_report
+        - params.limma_adjust_method
+        - params.limma_confint
+        - params.limma_lfc
+        - params.limma_method
+        - params.limma_p_value
+        - params.limma_proportion
+        - params.limma_robust
+        - params.limma_stdev_coef_lim
+        - params.limma_trend
+        - params.limma_use_voom
+        - params.limma_winsor_tail_p
+        - params.observations_id_col
+        - params.observations_type
+        - params.propd_fdr
+        - params.propd_moderated
+        - params.propd_number_of_cutoffs
+        - params.propd_permutation
+        - params.propd_save_adjacency
+        - params.propd_save_pairwise
+        - params.propd_save_pairwise_full
+        - params.propd_save_rdata
+        - params.proteus_measurecol_prefix
+        - params.proteus_norm_function
+        - params.proteus_palette_name
+        - params.proteus_plotmv_loess
+        - params.proteus_plotsd_method
+        - params.round_digits
+        - params.shinyngs_build_app
+        - params.shinyngs_deploy_to_shinyapps_io
+        - params.sizefactors_from_controls
+        - params.skip_reports
+        - params.study_abundance_type
+        - params.study_name
+        - params.study_type
+        - params.validate_params
+  # Every schema default is declared in main.nf rather than nextflow.config, so the schema/config
+  # comparison has nothing to compare.
+  schema_params: false
+  # Tests pass no `outdir` because the pipeline publishes with `-output-dir`.
+  nf_test_content:
+    - tests/default.nf.test
+    - tests/test_affy.nf.test
+    - tests/test_many.nf.test
+    - tests/test_maxquant.nf.test
+    - tests/test_nogtf.nf.test
+    - tests/test_rnaseq_deseq2.nf.test
+    - tests/test_rnaseq_dream.nf.test
+    - tests/test_rnaseq_limma.nf.test
+    - tests/test_rnaseq_propd_grea.nf.test
+    - tests/test_soft.nf.test
 nf_core_version: 4.0.2
 repository_type: pipeline
 template:

CHANGELOG.md

@@ -13,10 +13,12 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Changed
 
+- [[#758](https://github.com/nf-core/differentialabundance/pull/758)] - Make the pipeline a typed pipeline (`params {}` block, `output {}` block, files of a run as optional values) that can be included in another pipeline with Nextflow pipeline composition, with its own files located relative to the pipeline and the config params defaults in `conf/params.config`; the `--outdir` param is replaced by Nextflow's `-output-dir`, and the propd and grea results are published through the output block. ([@pinin4fjords](https://github.com/pinin4fjords))
 - [[#748](https://github.com/nf-core/differentialabundance/pull/748)] - Update `shinyngs` modules to 3.2.0 and modernise the Quarto report to use shinyngs 3.x plotting helpers, replacing hand-written PCA, clustering heatmap, top-gene boxplot, scree, upset, volcano and biotype code and reducing the report's container dependencies. ([@pinin4fjords](https://github.com/pinin4fjords)).
 
 ### Fixed
 
+- [[#758](https://github.com/nf-core/differentialabundance/pull/758)] - Apply the `cache = 'deep'` setting to the processes of the differential filter and functional enrichment subworkflows, which its selectors never matched, and allow profiles to unset `exploratory_log2_assays`. ([@pinin4fjords](https://github.com/pinin4fjords))
 - [[#747](https://github.com/nf-core/differentialabundance/pull/747)] - Fix silent contrast/result ordering mismatch in shinyngs Shiny app caused by `.sort().reverse()` in `collectFile` closures decoupling CSV row order from differential result file order. ([@jozsefkun](https://github.com/jozsefkun), review by [@pinin4fjords](https://github.com/pinin4fjords))
 
 ## v2.0.0 - 2026-05-26

README.md

@@ -10,7 +10,7 @@
 [![GitHub Actions Linting Status](https://github.com/nf-core/differentialabundance/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/differentialabundance/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/differentialabundance/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)
 [![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.7568000-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.7568000)
-[![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.10.4-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%A526.09.0--edge-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-4.0.2-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/4.0.2)
 [![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)
 [![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)
@@ -60,7 +60,7 @@ nextflow run nf-core/differentialabundance \
     --contrasts contrasts.yaml \
     --matrix assay_matrix.tsv \
     --gtf mouse.gtf \
-    --outdir <OUTDIR>
+    -output-dir <OUTDIR>
 ```
 
 > [!WARNING]
@@ -75,7 +75,7 @@ nextflow run nf-core/differentialabundance \
     --contrasts contrasts.yaml \
     --matrix assay_matrix.tsv \
     --gtf mouse.gtf \
-    --outdir <OUTDIR>
+    -output-dir <OUTDIR>
 ```
 
 > [!NOTE]
@@ -93,7 +93,7 @@ nextflow run nf-core/differentialabundance \
     --matrix assay_matrix.tsv \
     --gtf mouse.gtf \
     --gene_sets_files gene_sets.gmt \
-    --outdir <OUTDIR>
+    -output-dir <OUTDIR>
 ```
 
 Affymetrix microarray:
@@ -104,7 +104,7 @@ nextflow run nf-core/differentialabundance \
     --input samplesheet.csv \
     --contrasts contrasts.yaml \
     --affy_cel_files_archive cel_files.tar \
-    --outdir <OUTDIR>
+    -output-dir <OUTDIR>
 ```
 
 For full usage examples, analysis profiles, paramsheet-based multi-run mode, and input specifics (rnaseq counts, Affymetrix, MaxQuant, GEO SOFT), see the [usage documentation](https://nf-co.re/differentialabundance/usage) and the [parameter documentation](https://nf-co.re/differentialabundance/parameters).