Dev2Main - [1.6.0] - UNSC Trafalgar

.github/workflows/branch.yml

@@ -1,46 +1,24 @@
-name: nf-core branch protection
-# This workflow is triggered on PRs to `main`/`master` branch on the repository
-# It fails when someone tries to make a PR against the nf-core `main`/`master` branch instead of `dev`
+name: "Close user-tagged issues and PRs"
 on:
-  pull_request_target:
-    branches:
-      - main
-      - master
+  schedule:
+    - cron: "0 0 * * 0" # Once a week
 
 jobs:
-  test:
+  clean-up:
     runs-on: ubuntu-latest
+    permissions:
+      issues: write
+      pull-requests: write
     steps:
-      # PRs to the nf-core repo main/master branch are only ok if coming from the nf-core repo `dev` or any `patch` branches
-      - name: Check PRs
-        if: github.repository == 'sanger-tol/curationpretext'
-        run: |
-          { [[ ${{github.event.pull_request.head.repo.full_name }} == sanger-tol/curationpretext ]] && [[ $GITHUB_HEAD_REF == "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]]
-
-      # If the above check failed, post a comment on the PR explaining the failure
-      # NOTE - this doesn't currently work if the PR is coming from a fork, due to limitations in GitHub actions secrets
-      - name: Post PR comment
-        if: failure()
-        uses: mshick/add-pr-comment@b8f338c590a895d50bcbfa6c5859251edc8952fc # v2
+      - uses: actions/stale@5f858e3efba33a5ca4407a664cc011ad407f2008 # v10
         with:
-          message: |
-            ## This PR is against the `${{github.event.pull_request.base.ref}}` branch :x:
-
-            * Do not close this PR
-            * Click _Edit_ and change the `base` to `dev`
-            * This CI test will remain failed until you push a new commit
-
-            ---
-
-            Hi @${{ github.event.pull_request.user.login }},
-
-            It looks like this pull-request is has been made against the [${{github.event.pull_request.head.repo.full_name }}](https://github.com/${{github.event.pull_request.head.repo.full_name }}) ${{github.event.pull_request.base.ref}} branch.
-            The ${{github.event.pull_request.base.ref}} branch on nf-core repositories should always contain code from the latest release.
-            Because of this, PRs to ${{github.event.pull_request.base.ref}} are only allowed if they come from the [${{github.event.pull_request.head.repo.full_name }}](https://github.com/${{github.event.pull_request.head.repo.full_name }}) `dev` branch.
-
-            You do not need to close this PR, you can change the target branch to `dev` by clicking the _"Edit"_ button at the top of this page.
-            Note that even after this, the test will continue to show as failing until you push a new commit.
-
-            Thanks again for your contribution!
-          repo-token: ${{ secrets.GITHUB_TOKEN }}
-          allow-repeats: false
+          stale-issue-message: "This issue has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor. Remove stale label or add a comment otherwise this issue will be closed in 20 days."
+          stale-pr-message: "This PR has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor. Remove stale label or add a comment if it is still useful."
+          close-issue-message: "This issue was closed because it has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor and then staled for 20 days with no activity."
+          days-before-stale: 30
+          days-before-close: 20
+          days-before-pr-close: -1
+          any-of-labels: "awaiting-changes,awaiting-feedback"
+          exempt-issue-labels: "WIP"
+          exempt-pr-labels: "WIP"
+          repo-token: "${{ secrets.GITHUB_TOKEN }}"

.github/workflows/clean-up.yml

@@ -10,7 +10,7 @@ jobs:
       issues: write
       pull-requests: write
     steps:
-      - uses: actions/stale@5bef64f19d7facfb25b37b414482c7164d639639 # v9
+      - uses: actions/stale@5f858e3efba33a5ca4407a664cc011ad407f2008 # v10
         with:
           stale-issue-message: "This issue has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor. Remove stale label or add a comment otherwise this issue will be closed in 20 days."
           stale-pr-message: "This PR has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor. Remove stale label or add a comment if it is still useful."

.github/workflows/download_pipeline.yml

@@ -44,9 +44,9 @@ jobs:
       - name: Disk space cleanup
         uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
 
-      - uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5
+      - uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6
         with:
-          python-version: "3.13"
+          python-version: "3.14"
           architecture: "x64"
 
       - name: Setup Apptainer
@@ -57,7 +57,7 @@ jobs:
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install git+https://github.com/nf-core/tools.git@dev
+          pip install git+https://github.com/nf-core/tools.git
 
       - name: Make a cache directory for the container images
         run: |
@@ -127,7 +127,7 @@ jobs:
       #     fi
 
       # - name: Upload Nextflow logfile for debugging purposes
-      #   uses: actions/upload-artifact@ea165f8d65b6e75b540449e92b4886f43607fa02 # v4
+      #   uses: actions/upload-artifact@330a01c490aca151604b8cf639adc76d48f6c5d4 # v5
       #   with:
       #     name: nextflow_logfile.txt
       #     path: .nextflow.log*

.github/workflows/fix_linting.yml

@@ -13,13 +13,13 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       # Use the @nf-core-bot token to check out so we can push later
-      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
+      - uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
         with:
           token: ${{ secrets.nf_core_bot_auth_token }}
 
       # indication that the linting is being fixed
       - name: React on comment
-        uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4
+        uses: peter-evans/create-or-update-comment@e8674b075228eee787fea43ef493e45ece1004c9 # v5
         with:
           comment-id: ${{ github.event.comment.id }}
           reactions: eyes
@@ -32,9 +32,9 @@ jobs:
           GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }}
 
       # Install and run pre-commit
-      - uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5
+      - uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6
         with:
-          python-version: "3.13"
+          python-version: "3.14"
 
       - name: Install pre-commit
         run: pip install pre-commit
@@ -47,7 +47,7 @@ jobs:
       # indication that the linting has finished
       - name: react if linting finished succesfully
         if: steps.pre-commit.outcome == 'success'
-        uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4
+        uses: peter-evans/create-or-update-comment@e8674b075228eee787fea43ef493e45ece1004c9 # v5
         with:
           comment-id: ${{ github.event.comment.id }}
           reactions: "+1"
@@ -67,21 +67,21 @@ jobs:
       - name: react if linting errors were fixed
         id: react-if-fixed
         if: steps.commit-and-push.outcome == 'success'
-        uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4
+        uses: peter-evans/create-or-update-comment@e8674b075228eee787fea43ef493e45ece1004c9 # v5
         with:
           comment-id: ${{ github.event.comment.id }}
           reactions: hooray
 
       - name: react if linting errors were not fixed
         if: steps.commit-and-push.outcome == 'failure'
-        uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4
+        uses: peter-evans/create-or-update-comment@e8674b075228eee787fea43ef493e45ece1004c9 # v5
         with:
           comment-id: ${{ github.event.comment.id }}
           reactions: confused
 
       - name: react if linting errors were not fixed
         if: steps.commit-and-push.outcome  == 'failure'
-        uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4
+        uses: peter-evans/create-or-update-comment@e8674b075228eee787fea43ef493e45ece1004c9 # v5
         with:
           issue-number: ${{ github.event.issue.number }}
           body: |

.github/workflows/linting.yml

@@ -11,12 +11,12 @@ jobs:
   pre-commit:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
+      - uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
 
-      - name: Set up Python 3.13
-        uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5
+      - name: Set up Python 3.14
+        uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6
         with:
-          python-version: "3.13"
+          python-version: "3.14"
 
       - name: Install pre-commit
         run: pip install pre-commit
@@ -28,14 +28,14 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
+        uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
 
       - name: Install Nextflow
         uses: nf-core/setup-nextflow@v2
 
-      - uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5
+      - uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6
         with:
-          python-version: "3.13"
+          python-version: "3.14"
           architecture: "x64"
 
       - name: read .nf-core.yml
@@ -71,7 +71,7 @@ jobs:
 
       - name: Upload linting log file artifact
         if: ${{ always() }}
-        uses: actions/upload-artifact@ea165f8d65b6e75b540449e92b4886f43607fa02 # v4
+        uses: actions/upload-artifact@330a01c490aca151604b8cf639adc76d48f6c5d4 # v5
         with:
           name: linting-logs
           path: |

.github/workflows/linting_comment.yml

@@ -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@52423e01640425a022ef5fd42c6fb5f633a02728 # v2
+        uses: marocchino/sticky-pull-request-comment@773744901bac0e8cbb5a0dc842800d45e9b2b405 # v2
         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: "0.9.2"
+  NFT_VER: "0.9.3"
   NFT_WORKDIR: "~"
   NXF_ANSI_LOG: false
   NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity
@@ -39,7 +39,7 @@ jobs:
           rm -rf ./* || true
           rm -rf ./.??* || true
           ls -la ./
-      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
+      - uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
         with:
           fetch-depth: 0
 
@@ -76,14 +76,14 @@ jobs:
           - isMain: false
             profile: "singularity"
         NXF_VER:
-          - "24.10.5"
+          - "25.04.0"
           - "latest-everything"
     env:
       NXF_ANSI_LOG: false
       TOTAL_SHARDS: ${{ needs.nf-test-changes.outputs.total_shards }}
 
     steps:
-      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
+      - uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
         with:
           fetch-depth: 0
 
@@ -93,6 +93,7 @@ jobs:
         continue-on-error: ${{ matrix.NXF_VER == 'latest-everything' }}
         env:
           NFT_WORKDIR: ${{ env.NFT_WORKDIR }}
+          NXF_VERSION: ${{ matrix.NXF_VER }}
         with:
           profile: ${{ matrix.profile }}
           shard: ${{ matrix.shard }}

.github/workflows/template-version-comment.yml

@@ -9,7 +9,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
+        uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
         with:
           ref: ${{ github.event.pull_request.head.sha }}
 

.nf-core.yml

@@ -30,7 +30,7 @@ lint:
   nextflow_config:
     - manifest.name
     - manifest.homePage
-nf_core_version: 3.3.2
+nf_core_version: 3.5.2
 repository_type: pipeline
 template:
   author: Damon-Lee B Pointon (@DLBPointon)
@@ -48,4 +48,4 @@ template:
     - seqera_platform
     - multiqc
     - rocrate
-  version: 1.5.1
+  version: 1.6.0

.pre-commit-config.yaml

@@ -6,7 +6,7 @@ repos:
         additional_dependencies:
           - prettier@3.6.2
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v5.0.0
+    rev: v6.0.0
     hooks:
       - id: trailing-whitespace
         args: [--markdown-linebreak-ext=md]

.prettierignore

@@ -10,3 +10,6 @@ testing*
 *.pyc
 bin/
 CITATION.cff
+.nf-test/
+modules/nf-core/
+subworkflows/nf-core/

CHANGELOG.md

@@ -3,7 +3,69 @@
 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).
 
-## [[1.5.1]](https://github.com/sanger-tol/curationpretext/releases/tag/1.5.1)] - UNSC Punic (H1) - [2025-10-01]
+## [[1.6.0](https://github.com/sanger-tol/curationpretext/releases/tag/1.6.0)] - UNSC Trafalgar - [2025-02-19]
+
+## Added and Fixed
+
+- Template update to 3.5.2.
+- - The previous `GENERATE_MAPS` subworkflow has been replaced with `ALIGN_CRAM` and `CREATE_MAPS_{STDRD,HIRES}` (renamed from `CRAM_MAP_ILLUMINA_HIC` and `PAIRS_CREATE_CONTACT_MAPS`, from the [`sanger-tol/nf-core-modules`](https://github.com/sanger-tol/nf-core-modules) repository, respectively)
+- Files can now be given explicitly in the `--reads` parameter in the format of `[<file1>, <file2>, ...]`, alternatively it can accept a FOFN (File of file names).
+- Files can now be given explicitly in the `--cram` parameter in the format of `[<file1>, <file2>, ...]`, alternatively it can accept a FOFN (File of file names).
+- `--pre_mapped_bam` parameter added in order to supply 1 pre-mapped BAM file, in this case `--cram` would be empty.
+  - Warnings have been added to ensure:
+    - Only 1 pre-mapped BAM file is provided if `--pre_mapped_bam` is used.
+    - Only 1 of `--pre_mapped_bam` or `--cram` is used`
+- `--cram_chunk_size` parameter added by `ALIGN_CRAM` to make cram chunking configurable, defaulting to 10000.
+- `LONGREAD_COVERAGE` subworkflow has been updated to accept an array list of files.
+- Major Update to modules coinciding with changes to use Nextflow topics
+- Update to move all modules/subworkflows to version topics.
+  - Required a small change to the template topic collection otherwise it would fail as there is no ch_versions channel.
+- Update docs to include the features from the past few releases.
+- Remove duplicated `selected_aligner` code from `PIPELINE_INITIALISATION`.
+- Change install for `TELOMERE` modules so that we use the `SANGER-TOL` repository rather than local.
+- Removed now unused `bin` files.
+- Migrated from `local/telo_finder` subworkflow to `sanger-tol/telo_finder`.
+- Migrated from `local/gap_finder` subworkflow to `sanger-tol/gap_finder`.
+- Updated the schema to include patterns for the correct input file and to also allow fastq for reads along with fasta.
+
+### Parameters
+
+| Old Version | New Versions      |
+| ----------- | ----------------- |
+| NA          | --pre_mapped      |
+| NA          | --cram_chunk_size |
+
+### Software Dependencies
+
+Note, since the pipeline is using Nextflow DSL2, each process will be run with its own Biocontainer. This means that on occasion it is entirely possible for the pipeline to be using different versions of the same tool. However, the overall software dependency changes compared to the last release have been listed below for reference.
+
+| Module                         | Old Version      | New Versions                                                   |
+| ------------------------------ | ---------------- | -------------------------------------------------------------- |
+| `BEDTOOLS_BAMTOBED`            | 2.30.0           | 2.31.1                                                         |
+| `BEDTOOLS_GENOMECOV`           | 2.30.0           | 2.31.1                                                         |
+| `BEDTOOLS_INTERSECT`           | 2.30.0           | 2.31.1                                                         |
+| `BEDTOOLS_MAKEWINDOWS`         | 2.30.0           | 2.31.1                                                         |
+| `BEDTOOLS_MAP`                 | 2.30.0           | 2.31.1                                                         |
+| `CRAMALIGN_BWAMEM2ALIGNHIC`    | NEW_ADDITION     | bwamem2: 2.2.1, samtools: 1.22.1                               |
+| `GAWK`                         | 5.2.0            | 5.3.1                                                          |
+| `GNU_SORT`                     | 9.1              | 9.5                                                            |
+| `MINIMAP2_ALIGN`               | 2.28--he4a0461_0 | 2.29-r1283                                                     |
+| `PRETEXTMAP`                   | 0.1.9            | 0.1.9 (Temporary Patch, to be updated to 0.2.4 once available) |
+| `SAMTOOLS_FAIDX`               | 1.21.2           | 1.22.1                                                         |
+| `SAMTOOLS_MERGE`               | 1.21.2           | 1.22.1                                                         |
+| `SAMTOOLS_SORT`                | 1.21.2           | 1.22.1                                                         |
+| `SAMTOOLS_SPLITHEADER`         | 1.21.2           | 1.22.1                                                         |
+| `SAMTOOLS_VIEW_FILTER_PRIMARY` | 1.21.2           | 1.22.1                                                         |
+| `SAMTOOLS_MERGEDUP`            | NEW_ADDITION     | 1.23.0                                                         |
+| `FIND_TELOMERE_WINDOWS`        | 1.0.0            | REMOVED                                                        |
+| `TELOMERE_WINDOWS`             | NEW_ADDITION     | 1.0.0                                                          |
+| `FIND_TELOMERE_REGIONS`        | 1.0.0            | REMOVED                                                        |
+| `TELOMERE_REGIONS`             | NEW_ADDITION     | 1.0.0                                                          |
+| `EXTRACT_TELOMERE`             | 1.0.0            | REMOVED                                                        |
+| `TELOMERE_EXTRACT`             | NEW_ADDITION     | 1.0.0                                                          |
+| `UCSC_BEDGRAPHTOBIGWIG`        | 447              | 482                                                            |
+
+## [[1.5.1](https://github.com/sanger-tol/curationpretext/releases/tag/1.5.1)] - UNSC Punic (H1) - [2025-10-01]
 
 ### Added and Fixed