Merge pull request #243 from nf-core/dev

Release 2.2.0

Author: scwatts

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

@@ -54,13 +54,9 @@ runs:
         conda-solver: libmamba
         conda-remove-defaults: true
 
-      # TODO Skip failing conda tests and document their failures
-      # https://github.com/nf-core/modules/issues/7017
     - name: Run nf-test
       shell: bash
       env:
-        NFT_DIFF: ${{ env.NFT_DIFF }}
-        NFT_DIFF_ARGS: ${{ env.NFT_DIFF_ARGS }}
         NFT_WORKDIR: ${{ env.NFT_WORKDIR }}
       run: |
         nf-test test \

.github/workflows/linting.yml

@@ -13,7 +13,7 @@ jobs:
     steps:
       - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
 
-      - name: Set up Python 3.12
+      - name: Set up Python 3.13
         uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5
         with:
           python-version: "3.13"

.github/workflows/linting_comment.yml

@@ -11,7 +11,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Download lint results
-        uses: dawidd6/action-download-artifact@4c1e823582f43b179e2cbb49c3eade4e41f992e2 # v10
+        uses: dawidd6/action-download-artifact@ac66b43f0e6a346234dd65d4d0c8fbb31cb316e5 # v11
         with:
           workflow: linting.yml
           workflow_conclusion: completed

.github/workflows/nf-test.yml

@@ -1,12 +1,5 @@
 name: Run nf-test
 on:
-  push:
-    paths-ignore:
-      - "docs/**"
-      - "**/meta.yml"
-      - "**/*.md"
-      - "**/*.png"
-      - "**/*.svg"
   pull_request:
     paths-ignore:
       - "docs/**"
@@ -25,6 +18,7 @@ concurrency:
 
 env:
   GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+  NFT_TAGS: "cicd"
   NFT_VER: "0.9.2"
   NFT_WORKDIR: "~"
   NXF_ANSI_LOG: false
@@ -35,7 +29,7 @@ jobs:
   nf-test-changes:
     name: nf-test-changes
     runs-on: # use self-hosted runners
-      - runs-on=$-nf-test-changes
+      - runs-on=${{ github.run_id }}-nf-test-changes
       - runner=4cpu-linux-x64
     outputs:
       shard: ${{ steps.set-shards.outputs.shard }}
@@ -58,6 +52,7 @@ jobs:
           NFT_VER: ${{ env.NFT_VER }}
         with:
           max_shards: 7
+          tags: ${{ env.NFT_TAGS }}
 
       - name: debug
         run: |
@@ -69,7 +64,7 @@ jobs:
     needs: [nf-test-changes]
     if: ${{ needs.nf-test-changes.outputs.total_shards != '0' }}
     runs-on: # use self-hosted runners
-      - runs-on=$-nf-test
+      - runs-on=${{ github.run_id }}-nf-test
       - runner=4cpu-linux-x64
       - disk=large
     strategy:
@@ -86,7 +81,7 @@ jobs:
           - isMain: false
             profile: "singularity"
         NXF_VER:
-          - "24.04.2"
+          - "24.10.5"
           - "latest-everything"
     env:
       NXF_ANSI_LOG: false
@@ -98,23 +93,40 @@ jobs:
           fetch-depth: 0
 
       - name: Run nf-test
+        id: run_nf_test
         uses: ./.github/actions/nf-test
+        continue-on-error: ${{ matrix.NXF_VER == 'latest-everything' }}
         env:
-          NFT_DIFF: ${{ env.NFT_DIFF }}
-          NFT_DIFF_ARGS: ${{ env.NFT_DIFF_ARGS }}
           NFT_WORKDIR: ${{ env.NFT_WORKDIR }}
         with:
           profile: ${{ matrix.profile }}
           shard: ${{ matrix.shard }}
           total_shards: ${{ env.TOTAL_SHARDS }}
+          tags: ${{ env.NFT_TAGS }}
+
+      - name: Report test status
+        if: ${{ always() }}
+        run: |
+          if [[ "${{ steps.run_nf_test.outcome }}" == "failure" ]]; then
+            echo "::error::Test with ${{ matrix.NXF_VER }} failed"
+            # Add to workflow summary
+            echo "## ❌ Test failed: ${{ matrix.profile }} | ${{ matrix.NXF_VER }} | Shard ${{ matrix.shard }}/${{ env.TOTAL_SHARDS }}" >> $GITHUB_STEP_SUMMARY
+            if [[ "${{ matrix.NXF_VER }}" == "latest-everything" ]]; then
+              echo "::warning::Test with latest-everything failed but will not cause workflow failure. Please check if the error is expected or if it needs fixing."
+            fi
+            if [[ "${{ matrix.NXF_VER }}" != "latest-everything" ]]; then
+              exit 1
+            fi
+          fi
+
   confirm-pass:
     needs: [nf-test]
     if: always()
     runs-on: # use self-hosted runners
-      - runs-on=$-confirm-pass
+      - runs-on=${{ github.run_id }}-confirm-pass
       - runner=2cpu-linux-x64
     steps:
-      - name: One or more tests failed
+      - name: One or more tests failed (excluding latest-everything)
         if: ${{ contains(needs.*.result, 'failure') }}
         run: exit 1
 
@@ -133,11 +145,3 @@ jobs:
           echo "DEBUG: toJSON(needs) = ${{ toJSON(needs) }}"
           echo "DEBUG: toJSON(needs.*.result) = ${{ toJSON(needs.*.result) }}"
           echo "::endgroup::"
-
-      - name: Clean Workspace # Purge the workspace in case it's running on a self-hosted runner
-        if: always()
-        run: |
-          ls -la ./
-          rm -rf ./* || true
-          rm -rf ./.??* || true
-          ls -la ./

.github/workflows/release-announcements.yml

@@ -30,7 +30,7 @@ jobs:
   bsky-post:
     runs-on: ubuntu-latest
     steps:
-      - uses: zentered/bluesky-post-action@4aa83560bb3eac05dbad1e5f221ee339118abdd2 # v0.2.0
+      - uses: zentered/bluesky-post-action@6461056ea355ea43b977e149f7bf76aaa572e5e8 # v0.3.0
         with:
           post: |
             Pipeline release! ${{ github.repository }} v${{ github.event.release.tag_name }} - ${{ github.event.release.name }}!

.nf-core.yml

@@ -1,5 +1,5 @@
 repository_type: pipeline
-nf_core_version: 3.3.1
+nf_core_version: 3.3.2
 template:
   author: Stephen Watts
   description: A comprehensive cancer DNA/RNA analysis and reporting pipeline
@@ -8,13 +8,12 @@ template:
   name: oncoanalyser
   org: nf-core
   outdir: .
-  version: 2.1.0
   skip_features:
+    - gpu
     - nf-test
+  version: 2.2.0
 lint:
   actions_ci: false
-  multiqc_config: false
-  nf_test_content: false
   files_exist:
     - lib/Utils.groovy
     - lib/WorkflowMain.groovy
@@ -23,7 +22,9 @@ lint:
     - assets/nf-core-oncoanalyser_logo_light.png
     - docs/images/nf-core-oncoanalyser_logo_dark.png
     - docs/images/nf-core-oncoanalyser_logo_light.png
+  multiqc_config: false
   nextflow_config:
     - config_defaults:
         - params.fastp_umi_length
         - params.fastp_umi_skip
+  nf_test_content: false

.pre-commit-config.yaml

@@ -4,7 +4,7 @@ repos:
     hooks:
       - id: prettier
         additional_dependencies:
-          - prettier@3.5.0
+          - prettier@3.6.2
   - repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v5.0.0
     hooks:

CHANGELOG.md

@@ -3,6 +3,67 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) and this project mostly adheres to
 [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [[2.2.0](https://github.com/nf-core/oncoanalyser/releases/tag/2.2.0)] Royal Spoonbill - 2025-08-02
+
+- [241](https://github.com/nf-core/oncoanalyser/pull/241) - Apply minor fixes and updates
+  - Allow 'prepare reference' feature to be driven by samplesheet
+  - Set minimum stringr / stringi version for CUPPA environment
+  - Reintroduce decoy sequences for ESVEE with GRCh37 genomes
+  - Update WiGiTS reference data paths
+  - Improve FASTQ and longitudinal sample input handling
+  - Fix REDUX TSV collection in SAGE append subworkflow
+  - Update CHANGELOG.md
+- [235](https://github.com/nf-core/oncoanalyser/pull/235) - Publish selected command / log files
+- [234](https://github.com/nf-core/oncoanalyser/pull/234) - Update WiGiTS tools and reference data
+- [233](https://github.com/nf-core/oncoanalyser/pull/233) - Update documentation
+- [232](https://github.com/nf-core/oncoanalyser/pull/232) - Extend the 'prepare reference' functionality
+- [231](https://github.com/nf-core/oncoanalyser/pull/231) - Implement 'purity estimate' (WISP) workflow
+- [230](https://github.com/nf-core/oncoanalyser/pull/230) - Implement 'panel resource creation' workflow
+- [220](https://github.com/nf-core/oncoanalyser/pull/220) - Add reports to tower.yml
+- [222](https://github.com/nf-core/oncoanalyser/pull/222) - Post-release bump
+
+### Software dependencies
+
+| Dependency         | Old version | New version |
+| ------------------ | ----------- | ----------- |
+| `AMBER`            | 4.1.1       | 4.2         |
+| `BamTools`         | 1.3         | 1.4.2       |
+| `bwa-plus`         | 1.0.0       | -           |
+| `bwa-mem2`         | -           | 2.3         |
+| `CHORD`            | 2.1.0       | 2.1.2       |
+| `COBALT`           | 2.0         | 2.1         |
+| `ESVEE`            | 1.0.3       | 1.1.2       |
+| `ISOFOX`           | 1.7.1       | 1.7.2       |
+| `LILAC`            | 1.6         | 1.7.1       |
+| `LINX`             | 2.0.2       | 2.1         |
+| `NEO`              | 1.2         | 1.2.1       |
+| `ORANGE`           | 3.8.1       | 4.1         |
+| `PAVE`             | 1.7.1       | 1.8         |
+| `PURPLE`           | 4.1         | 4.2         |
+| `REDUX`            | 1.1.2       | 1.2         |
+| `SAGE`             | 4.0         | 4.1         |
+| `VirusInterpreter` | 1.7         | 1.7.1       |
+| `WISP`             | -           | 1.2         |
+
+### Reference data
+
+| Name                     | Old version | New version |
+| ------------------------ | ----------- | ----------- |
+| `HMF pipeline resources` | `2.1.0--1`  | `2.2.0--3`  |
+| `HMF TSO500 resources`   | `2.0.0--3`  | `2.2.0--3`  |
+
+### Parameters
+
+| Old name    | New name               |
+| ----------- | ---------------------- |
+| `fastp_umi` | `fastp_umi_enabled`    |
+| `redux_umi` | `redux_umi_enabled`    |
+| -           | `purity_estimate_mode` |
+| -           | `ref_data_types`       |
+| -           | `driver_gene_panel`    |
+| -           | `target_regions_bed`   |
+| -           | `hmftools_log_level`   |
+
 ## [[2.1.0](https://github.com/nf-core/oncoanalyser/releases/tag/2.1.0)] Peruvian Pelican - 2025-06-30
 
 - [219](https://github.com/nf-core/oncoanalyser/pull/219) - Add metromap-style diagram for pipeline overview

README.md

@@ -5,14 +5,14 @@
   </picture>
 </h1>
 
-[![GitHub Actions CI Status](https://github.com/nf-core/oncoanalyser/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-core/oncoanalyser/actions/workflows/ci.yml)
+[![GitHub Actions CI Status](https://github.com/nf-core/oncoanalyser/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/oncoanalyser/actions/workflows/nf-test.yml)
 [![GitHub Actions Linting Status](https://github.com/nf-core/oncoanalyser/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/oncoanalyser/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/oncoanalyser/results)
 [![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.15189386-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.15189386)
 [![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%A524.04.2-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-3.3.1-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.3.1)
+[![Nextflow](https://img.shields.io/badge/version-%E2%89%A524.10.5-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-3.3.2-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.3.2)
 [![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/)
 [![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)
@@ -25,27 +25,35 @@
 
 ## Introduction
 
-**nf-core/oncoanalyser** is a Nextflow pipeline for the comprehensive analysis of cancer genomes and transcriptomes
+**nf-core/oncoanalyser** is a Nextflow pipeline for the comprehensive analysis of cancer DNA and RNA sequencing data
 using the [WiGiTS](https://github.com/hartwigmedical/hmftools) toolkit from the Hartwig Medical Foundation. The pipeline
 supports a wide range of experimental setups:
 
-- FASTQ, BAM, or CRAM input files
-- WGS (whole genome sequencing), WTS (whole transcriptome sequencing), and targeted / panel sequencing (built-in support
-  for the [TSO500
-  panel](https://sapac.illumina.com/products/by-type/clinical-research-products/trusight-oncology-500.html) with other
-  panels and exome requiring [panel reference data
-  generation](https://github.com/hartwigmedical/hmftools/blob/master/pipeline/README_TARGETED.md))
-- Paired tumor / normal and tumor-only sample setups, donor sample support for further normal subtraction (e.g. for
-  patients with bone marrow transplants or other contaminants in the tumor)
+- FASTQ, BAM, and / or CRAM input files
+- WGS (whole genome sequencing), WTS (whole transcriptome sequencing), and targeted / panel sequencing<sup>1</sup>
+- Paired tumor / normal and tumor-only samples, and support for donor samples for further normal subtraction
+- Purity estimate for longitudinal samples using genomic features of the primary sample from the same patient<sup>2</sup>
 - UMI (unique molecular identifier) processing supported for DNA sequencing data
 - Most GRCh37 and GRCh38 reference genome builds
 
+<sub><sup>1</sup> built-in support for the [TSO500
+panel](https://www.illumina.com/products/by-type/clinical-research-products/trusight-oncology-500.html) with other
+panels and exomes requiring [creation of custom panel reference
+data](https://nf-co.re/oncoanalyser/usage#custom-panels)</sub>
+<br />
+<sub><sup>2</sup> for example a primary WGS tissue biospy and longitudinal low-pass WGS ccfDNA sample taken from the
+same patient</sub>
+
 ## Pipeline overview
 
 <p align="center"><img src="docs/images/oncoanalyser_pipeline.png"></p>
 
-The pipeline mainly uses tools from [WiGiTS](https://github.com/hartwigmedical/hmftools), as well as some external
-tools. Due to the limitations of panel data, certain tools (indicated with `*` below) do not run in `targeted` mode.
+The pipeline mainly uses tools from [WiGiTS](https://github.com/hartwigmedical/hmftools), as well as some other external
+tools. There are [several workflows available](https://nf-co.re/oncoanalyser/usage#introduction) in `oncoanalyser` and
+the tool information below primarily relates to the `wgts` and `targeted` analysis modes.
+
+> [!NOTE]
+> Due to the limitations of panel data, certain tools (indicated with `*` below) do not run in `targeted` mode.
 
 - Read alignment: [BWA-MEM2](https://github.com/bwa-mem2/bwa-mem2) (DNA), [STAR](https://github.com/alexdobin/STAR) (RNA)
 - Read post-processing: [REDUX](https://github.com/hartwigmedical/hmftools/tree/master/redux) (DNA), [Picard MarkDuplicates](https://gatk.broadinstitute.org/hc/en-us/articles/360037052812-MarkDuplicates-Picard) (RNA)
@@ -63,6 +71,10 @@ tools. Due to the limitations of panel data, certain tools (indicated with `*` b
 - Pharmacogenomics: [PEACH](https://github.com/hartwigmedical/hmftools/tree/master/peach)
 - Summary report: [ORANGE](https://github.com/hartwigmedical/hmftools/tree/master/orange), [linxreport](https://github.com/umccr/linxreport)
 
+For the `purity_estimate` mode, several of the above tools are run with adjusted configuration in addition to the following.
+
+- Tumor fraction estimation: [WISP](https://github.com/hartwigmedical/hmftools/tree/master/wisp)
+
 ## Usage
 
 > [!NOTE]
@@ -82,7 +94,7 @@ Launch `oncoanalyser`:
 ```bash
 nextflow run nf-core/oncoanalyser \
   -profile <docker/singularity/.../institute> \
-  -revision 2.1.0 \
+  -revision 2.2.0 \
   --mode <wgts/targeted> \
   --genome <GRCh37_hmf/GRCh38_hmf> \
   --input samplesheet.csv \

conf/base.config

@@ -63,5 +63,6 @@ process {
     }
     withLabel: process_gpu {
         ext.use_gpu = { workflow.profile.contains('gpu') }
+        accelerator = { workflow.profile.contains('gpu') ? 1 : null }
     }
 }