diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json
index b290e09..97c8c97 100644
--- a/.devcontainer/devcontainer.json
+++ b/.devcontainer/devcontainer.json
@@ -1,20 +1,20 @@
{
"name": "nfcore",
- "image": "nfcore/gitpod:latest",
- "remoteUser": "gitpod",
- "runArgs": ["--privileged"],
+ "image": "nfcore/devcontainer:latest",
- // Configure tool-specific properties.
- "customizations": {
- // Configure properties specific to VS Code.
- "vscode": {
- // Set *default* container specific settings.json values on container create.
- "settings": {
- "python.defaultInterpreterPath": "/opt/conda/bin/python"
- },
+ "remoteUser": "root",
+ "privileged": true,
- // Add the IDs of extensions you want installed when the container is created.
- "extensions": ["ms-python.python", "ms-python.vscode-pylance", "nf-core.nf-core-extensionpack"]
- }
+ "remoteEnv": {
+ // Workspace path on the host for mounting with docker-outside-of-docker
+ "LOCAL_WORKSPACE_FOLDER": "${localWorkspaceFolder}"
+ },
+
+ "onCreateCommand": "./.devcontainer/setup.sh",
+
+ "hostRequirements": {
+ "cpus": 4,
+ "memory": "16gb",
+ "storage": "32gb"
}
}
diff --git a/.devcontainer/setup.sh b/.devcontainer/setup.sh
new file mode 100755
index 0000000..d7b3757
--- /dev/null
+++ b/.devcontainer/setup.sh
@@ -0,0 +1,13 @@
+#!/usr/bin/env bash
+
+# Customise the terminal command prompt
+echo "export PROMPT_DIRTRIM=2" >> $HOME/.bashrc
+echo "export PS1='\[\e[3;36m\]\w ->\[\e[0m\\] '" >> $HOME/.bashrc
+export PROMPT_DIRTRIM=2
+export PS1='\[\e[3;36m\]\w ->\[\e[0m\\] '
+
+# Update Nextflow
+nextflow self-update
+
+# Update welcome message
+echo "Welcome to the qbic-pipelines/vcftomaf devcontainer!" > /usr/local/etc/vscode-dev-containers/first-run-notice.txt
diff --git a/.editorconfig b/.editorconfig
deleted file mode 100644
index 6d9b74c..0000000
--- a/.editorconfig
+++ /dev/null
@@ -1,37 +0,0 @@
-root = true
-
-[*]
-charset = utf-8
-end_of_line = lf
-insert_final_newline = true
-trim_trailing_whitespace = true
-indent_size = 4
-indent_style = space
-
-[*.{md,yml,yaml,html,css,scss,js}]
-indent_size = 2
-
-# These files are edited and tested upstream in nf-core/modules
-[/modules/nf-core/**]
-charset = unset
-end_of_line = unset
-insert_final_newline = unset
-trim_trailing_whitespace = unset
-indent_style = unset
-[/subworkflows/nf-core/**]
-charset = unset
-end_of_line = unset
-insert_final_newline = unset
-trim_trailing_whitespace = unset
-indent_style = unset
-
-[/assets/email*]
-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
diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md
index 65ad238..8ff5742 100644
--- a/.github/CONTRIBUTING.md
+++ b/.github/CONTRIBUTING.md
@@ -71,7 +71,7 @@ If you wish to contribute a new step, please use the following coding standards:
5. Add any new parameters to `nextflow_schema.json` with help text (via the `nf-core pipelines schema build` tool).
6. Add sanity checks and validation for all relevant parameters.
7. Perform local tests to validate that the new code works as expected.
-8. If applicable, add a new test command in `.github/workflow/ci.yml`.
+8. If applicable, add a new test in the `tests` directory.
9. Update MultiQC config `assets/multiqc_config.yml` so relevant suffixes, file name clean up and module plots are in the appropriate order. If applicable, add a [MultiQC](https://https://multiqc.info/) module.
10. Add a description of the output files and if relevant any appropriate images from the MultiQC report to `docs/output.md`.
diff --git a/.github/actions/get-shards/action.yml b/.github/actions/get-shards/action.yml
index 3de9f39..3408527 100644
--- a/.github/actions/get-shards/action.yml
+++ b/.github/actions/get-shards/action.yml
@@ -9,7 +9,7 @@ inputs:
required: false
tags:
description: "Tags to pass as argument for nf-test --tag parameter"
- required: true
+ required: false
outputs:
shard:
description: "Array of shard numbers"
@@ -31,7 +31,7 @@ runs:
# Run nf-test with dynamic parameter
nftest_output=$(nf-test test \
--profile +docker \
- --tag ${{ inputs.tags }} \
+ $(if [ -n "${{ inputs.tags }}" ]; then echo "--tag ${{ inputs.tags }}"; fi) \
--dry-run \
--ci \
--changed-since HEAD^) || {
diff --git a/.github/actions/nf-test/action.yml b/.github/actions/nf-test/action.yml
index fd04364..3b9724c 100644
--- a/.github/actions/nf-test/action.yml
+++ b/.github/actions/nf-test/action.yml
@@ -15,7 +15,7 @@ inputs:
required: true
tags:
description: "Tags to pass as argument for nf-test --tag parameter"
- required: true
+ required: false
runs:
using: "composite"
steps:
@@ -25,14 +25,15 @@ runs:
version: "${{ env.NXF_VERSION }}"
- name: Set up Python
- uses: actions/setup-python@42375524e23c412d93fb67b49958b491fce71c38 # v5
+ uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6
with:
- python-version: "3.11"
+ python-version: "3.14"
- name: Install nf-test
uses: nf-core/setup-nf-test@v1
with:
version: "${{ env.NFT_VER }}"
+ install-pdiff: true
- name: Setup apptainer
if: contains(inputs.profile, 'singularity')
@@ -46,38 +47,28 @@ runs:
mkdir -p $NXF_SINGULARITY_LIBRARYDIR
- name: Conda setup
- if: ${{inputs.profile == 'conda'}}
+ if: contains(inputs.profile, 'conda')
uses: conda-incubator/setup-miniconda@505e6394dae86d6a5c7fbb6e3fb8938e3e863830 # v3
with:
auto-update-conda: true
conda-solver: libmamba
+ channels: conda-forge
+ channel-priority: strict
conda-remove-defaults: true
- - name: Install pdiff
- shell: bash
- run: |
- python -m pip install pdiff
-
- - name: Clean up Disk space
- uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
-
- # 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: ${{ env.NFT_WORKDIR }}
run: |
nf-test test \
--profile=+${{ inputs.profile }} \
- --tag ${{ inputs.tags }} \
- --tap=test.tap \
- --verbose \
+ $(if [ -n "${{ inputs.tags }}" ]; then echo "--tag ${{ inputs.tags }}"; fi) \
--ci \
--changed-since HEAD^ \
- --shard ${{ inputs.shard }}/${{ inputs.total_shards }} \
+ --verbose \
+ --tap=test.tap \
+ --shard ${{ inputs.shard }}/${{ inputs.total_shards }}
# Save the absolute path of the test.tap file to the output
echo "tap_file_path=$(realpath test.tap)" >> $GITHUB_OUTPUT
diff --git a/.github/workflows/clean-up.yml b/.github/workflows/clean-up.yml
index 0b6b1f2..6adb0ff 100644
--- a/.github/workflows/clean-up.yml
+++ b/.github/workflows/clean-up.yml
@@ -10,7 +10,7 @@ jobs:
issues: write
pull-requests: write
steps:
- - uses: actions/stale@28ca1036281a5e5922ead5184a1bbf96e5fc984e # v9
+ - uses: actions/stale@5f858e3efba33a5ca4407a664cc011ad407f2008 # v10
with:
stale-issue-message: "This issue has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor. Remove stale label or add a comment otherwise this issue will be closed in 20 days."
stale-pr-message: "This PR has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor. Remove stale label or add a comment if it is still useful."
diff --git a/.github/workflows/download_pipeline.yml b/.github/workflows/download_pipeline.yml
index f60afc0..5462a06 100644
--- a/.github/workflows/download_pipeline.yml
+++ b/.github/workflows/download_pipeline.yml
@@ -12,14 +12,6 @@ on:
required: true
default: "dev"
pull_request:
- types:
- - opened
- - edited
- - synchronize
- branches:
- - main
- - master
- pull_request_target:
branches:
- main
- master
@@ -52,9 +44,9 @@ jobs:
- name: Disk space cleanup
uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
- - uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
+ - uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6
with:
- python-version: "3.12"
+ python-version: "3.14"
architecture: "x64"
- name: Setup Apptainer
@@ -65,7 +57,7 @@ jobs:
- name: Install dependencies
run: |
python -m pip install --upgrade pip
- pip install git+https://github.com/nf-core/tools.git@dev
+ pip install git+https://github.com/nf-core/tools.git
- name: Make a cache directory for the container images
run: |
@@ -120,6 +112,7 @@ jobs:
echo "IMAGE_COUNT_AFTER=$image_count" >> "$GITHUB_OUTPUT"
- name: Compare container image counts
+ id: count_comparison
run: |
if [ "${{ 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 }}
@@ -131,4 +124,11 @@ jobs:
exit 1
else
echo "The pipeline can be downloaded successfully!"
- fi{% endraw %}{% endif %}
+ fi
+
+ - name: Upload Nextflow logfile for debugging purposes
+ uses: actions/upload-artifact@330a01c490aca151604b8cf639adc76d48f6c5d4 # v5
+ with:
+ name: nextflow_logfile.txt
+ path: .nextflow.log*
+ include-hidden-files: true
diff --git a/.github/workflows/fix-linting.yml b/.github/workflows/fix_linting.yml
similarity index 80%
rename from .github/workflows/fix-linting.yml
rename to .github/workflows/fix_linting.yml
index a820858..6fbf0e2 100644
--- a/.github/workflows/fix-linting.yml
+++ b/.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@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
+ - uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6
with:
- python-version: "3.12"
+ 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: |
diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml
index dbd52d5..7a527a3 100644
--- a/.github/workflows/linting.yml
+++ b/.github/workflows/linting.yml
@@ -3,9 +3,6 @@ name: nf-core linting
# It runs the `nf-core pipelines lint` and markdown lint tests to ensure
# that the code meets the nf-core guidelines.
on:
- push:
- branches:
- - dev
pull_request:
release:
types: [published]
@@ -14,12 +11,12 @@ jobs:
pre-commit:
runs-on: ubuntu-latest
steps:
- - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
+ - uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
- - name: Set up Python 3.12
- uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
+ - name: Set up Python 3.14
+ uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6
with:
- python-version: "3.12"
+ python-version: "3.14"
- name: Install pre-commit
run: pip install pre-commit
@@ -31,18 +28,18 @@ 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@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
+ - uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6
with:
- python-version: "3.12"
+ python-version: "3.14"
architecture: "x64"
- name: read .nf-core.yml
- uses: pietrobolcato/action-read-yaml@1.1.0
+ uses: pietrobolcato/action-read-yaml@9f13718d61111b69f30ab4ac683e67a56d254e1d # 1.1.0
id: read_yml
with:
config: ${{ github.workspace }}/.nf-core.yml
@@ -74,7 +71,7 @@ jobs:
- name: Upload linting log file artifact
if: ${{ always() }}
- uses: actions/upload-artifact@b4b15b8c7c6ac21ea08fcf65892d2ee8f75cf882 # v4
+ uses: actions/upload-artifact@330a01c490aca151604b8cf639adc76d48f6c5d4 # v5
with:
name: linting-logs
path: |
diff --git a/.github/workflows/linting_comment.yml b/.github/workflows/linting_comment.yml
index 95b6b6a..e6e9bc2 100644
--- a/.github/workflows/linting_comment.yml
+++ b/.github/workflows/linting_comment.yml
@@ -11,7 +11,7 @@ jobs:
runs-on: ubuntu-latest
steps:
- name: Download lint results
- uses: dawidd6/action-download-artifact@20319c5641d495c8a52e688b7dc5fada6c3a9fbc # v8
+ uses: dawidd6/action-download-artifact@ac66b43f0e6a346234dd65d4d0c8fbb31cb316e5 # v11
with:
workflow: linting.yml
workflow_conclusion: completed
@@ -21,7 +21,7 @@ jobs:
run: echo "pr_number=$(cat linting-logs/PR_number.txt)" >> $GITHUB_OUTPUT
- name: Post PR comment
- uses: marocchino/sticky-pull-request-comment@331f8f5b4215f0445d3c07b4967662a32a2d3e31 # v2
+ uses: marocchino/sticky-pull-request-comment@773744901bac0e8cbb5a0dc842800d45e9b2b405 # v2
with:
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
number: ${{ steps.pr_number.outputs.pr_number }}
diff --git a/.github/workflows/nf-test.yml b/.github/workflows/nf-test.yml
index e9d6d9a..7fd88b5 100644
--- a/.github/workflows/nf-test.yml
+++ b/.github/workflows/nf-test.yml
@@ -1,29 +1,15 @@
name: Run nf-test
on:
- push:
- paths-ignore:
- - "docs/**"
- - "**/meta.yml"
- - "**/*.md"
- - "**/*.png"
- - "**/*.svg"
pull_request:
- branches: [dev]
paths-ignore:
- "docs/**"
- "**/meta.yml"
- "**/*.md"
- "**/*.png"
- "**/*.svg"
+ release:
+ types: [published]
workflow_dispatch:
- inputs:
- runners:
- description: "Runners to test on"
- type: choice
- options:
- - "ubuntu-latest"
- - "self-hosted"
- default: "ubuntu-latest"
# Cancel if a newer run is started
concurrency:
@@ -32,9 +18,7 @@ concurrency:
env:
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
- NFT_DIFF: "pdiff"
- NFT_DIFF_ARGS: "--line-numbers --width 120 --expand-tabs=2"
- NFT_VER: "0.9.2"
+ NFT_VER: "0.9.3"
NFT_WORKDIR: "~"
NXF_ANSI_LOG: false
NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity
@@ -43,7 +27,8 @@ env:
jobs:
nf-test-changes:
name: nf-test-changes
- runs-on: ${{ github.event.inputs.runners || github.run_number > 1 && 'ubuntu-latest' || 'self-hosted' }}
+ runs-on: # use GitHub runners
+ - "ubuntu-latest"
outputs:
shard: ${{ steps.set-shards.outputs.shard }}
total_shards: ${{ steps.set-shards.outputs.total_shards }}
@@ -54,7 +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
@@ -64,8 +49,7 @@ jobs:
env:
NFT_VER: ${{ env.NFT_VER }}
with:
- max_shards: 15
- tags: "cpu"
+ max_shards: 7
- name: debug
run: |
@@ -73,52 +57,70 @@ jobs:
echo ${{ steps.set-shards.outputs.total_shards }}
nf-test:
- runs-on: ${{ github.event.inputs.runners || github.run_number > 1 && 'ubuntu-latest' || 'self-hosted' }}
name: "${{ matrix.profile }} | ${{ matrix.NXF_VER }} | ${{ matrix.shard }}/${{ needs.nf-test-changes.outputs.total_shards }}"
needs: [nf-test-changes]
if: ${{ needs.nf-test-changes.outputs.total_shards != '0' }}
+ runs-on: # use GitHub runners
+ - "ubuntu-latest"
strategy:
fail-fast: false
matrix:
shard: ${{ fromJson(needs.nf-test-changes.outputs.shard) }}
profile: [conda, docker, singularity]
- isMaster:
- - ${{ github.base_ref == 'master' }}
+ isMain:
+ - ${{ github.base_ref == 'master' || github.base_ref == 'main' }}
# Exclude conda and singularity on dev
exclude:
- - isMaster: false
+ - isMain: false
profile: "conda"
- - isMaster: false
+ - isMain: false
profile: "singularity"
NXF_VER:
- - "24.10.2"
+ - "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
- 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 }}
+ NXF_VERSION: ${{ matrix.NXF_VER }}
with:
profile: ${{ matrix.profile }}
shard: ${{ matrix.shard }}
total_shards: ${{ env.TOTAL_SHARDS }}
- tags: "cpu"
+
+ - 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:
- runs-on: ${{ github.event.inputs.runners || github.run_number > 1 && 'ubuntu-latest' || 'self-hosted' }}
needs: [nf-test]
if: always()
+ runs-on: # use GitHub runners
+ - "ubuntu-latest"
steps:
- - name: One or more tests failed
+ - name: One or more tests failed (excluding latest-everything)
if: ${{ contains(needs.*.result, 'failure') }}
run: exit 1
@@ -137,11 +139,3 @@ 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 ./
diff --git a/.github/workflows/template_version_comment.yml b/.github/workflows/template-version-comment.yml
similarity index 91%
rename from .github/workflows/template_version_comment.yml
rename to .github/workflows/template-version-comment.yml
index 537529b..e8560fc 100644
--- a/.github/workflows/template_version_comment.yml
+++ b/.github/workflows/template-version-comment.yml
@@ -9,12 +9,12 @@ 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 }}
- name: Read template version from .nf-core.yml
- uses: nichmor/minimal-read-yaml@v0.0.2
+ uses: nichmor/minimal-read-yaml@1f7205277e25e156e1f63815781db80a6d490b8f # v0.0.2
id: read_yml
with:
config: ${{ github.workspace }}/.nf-core.yml
diff --git a/.gitpod.yml b/.gitpod.yml
deleted file mode 100644
index 7d7107c..0000000
--- a/.gitpod.yml
+++ /dev/null
@@ -1,13 +0,0 @@
-image: nfcore/gitpod:latest
-tasks:
- - name: Update Nextflow and setup pre-commit
- command: |
- pre-commit install --install-hooks
- nextflow self-update
- - name: unset JAVA_TOOL_OPTIONS
- command: |
- unset JAVA_TOOL_OPTIONS
-
-vscode:
- extensions:
- - nf-core.nf-core-extensionpack # https://github.com/nf-core/vscode-extensionpack
diff --git a/.nf-core.yml b/.nf-core.yml
index b4a8033..3db59df 100644
--- a/.nf-core.yml
+++ b/.nf-core.yml
@@ -27,7 +27,7 @@ lint:
nextflow_config:
- manifest.name
- manifest.homePage
-nf_core_version: 3.2.1
+nf_core_version: 3.5.1
repository_type: pipeline
template:
author: SusiJo, FriederikeHanssen, famosab
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 1dec865..d06777a 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -4,10 +4,24 @@ repos:
hooks:
- id: prettier
additional_dependencies:
- - prettier@3.2.5
-
- - repo: https://github.com/editorconfig-checker/editorconfig-checker.python
- rev: "3.1.2"
+ - prettier@3.6.2
+ - repo: https://github.com/pre-commit/pre-commit-hooks
+ rev: v6.0.0
hooks:
- - id: editorconfig-checker
- alias: ec
+ - id: trailing-whitespace
+ args: [--markdown-linebreak-ext=md]
+ exclude: |
+ (?x)^(
+ .*ro-crate-metadata.json$|
+ modules/nf-core/.*|
+ subworkflows/nf-core/.*|
+ .*\.snap$
+ )$
+ - id: end-of-file-fixer
+ exclude: |
+ (?x)^(
+ .*ro-crate-metadata.json$|
+ modules/nf-core/.*|
+ subworkflows/nf-core/.*|
+ .*\.snap$
+ )$
diff --git a/.prettierignore b/.prettierignore
index edd29f0..dd749d4 100644
--- a/.prettierignore
+++ b/.prettierignore
@@ -10,4 +10,7 @@ testing/
testing*
*.pyc
bin/
+.nf-test/
ro-crate-metadata.json
+modules/nf-core/
+subworkflows/nf-core/
diff --git a/.prettierrc.yml b/.prettierrc.yml
index c81f9a7..07dbd8b 100644
--- a/.prettierrc.yml
+++ b/.prettierrc.yml
@@ -1 +1,6 @@
printWidth: 120
+tabWidth: 4
+overrides:
+ - files: "*.{md,yml,yaml,html,css,scss,js,cff}"
+ options:
+ tabWidth: 2
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 23e2e8c..fb1b809 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -14,11 +14,13 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- [#34](https://github.com/qbic-pipelines/vcftomaf/pull/34) - Update vcf2maf configuration to adhere to hg38 as reference genome (@famosab)
- [#35](https://github.com/qbic-pipelines/vcftomaf/pull/35) - Template update to 3.2.0 (@famosab)
- [#37](https://github.com/qbic-pipelines/vcftomaf/pull/37) - Template update to 3.2.1 (@famosab)
+- [#38](https://github.com/qbic-pipelines/vcftomaf/pull/38) - Template update to 3.5.1 (@famosab)
### `Dependencies`
| Dependency | Old version | New version |
| ---------- | ----------- | ----------- |
+| MultiQC | 1.25.1 | 1.32 |
### `Deprecated`
diff --git a/Dockerfile b/Dockerfile
index 680368a..d4e7e83 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -14,4 +14,3 @@ RUN apt-get update -qq
ENV PATH /opt/conda/envs/qbic-pipelines-vcftomaf-dev/bin:$PATH
# Dump the details of the installed packates to a file for posterity
RUN mamba env export --name qbic-pipelines-vcftomaf-dev > qbic-pipelines-vcftomaf-dev.yml
-
diff --git a/README.md b/README.md
index e93e829..c05a5f0 100644
--- a/README.md
+++ b/README.md
@@ -1,10 +1,12 @@
#  
-[](https://github.com/qbic-pipelines/vcftomaf/actions/workflows/ci.yml)
+[](https://github.com/codespaces/new/qbic-pipelines/vcftomaf)
+[](https://github.com/qbic-pipelines/vcftomaf/actions/workflows/nf-test.yml)
[](https://github.com/qbic-pipelines/vcftomaf/actions/workflows/linting.yml)[](https://doi.org/10.5281/zenodo.10812762)
[](https://www.nf-test.com)
-[](https://www.nextflow.io/)
+[](https://www.nextflow.io/)
+[](https://github.com/nf-core/tools/releases/tag/3.5.1)
[](https://docs.conda.io/en/latest/)
[](https://www.docker.com/)
[](https://sylabs.io/docs/)
diff --git a/conf/base.config b/conf/base.config
index 0bebd7e..333f3dc 100644
--- a/conf/base.config
+++ b/conf/base.config
@@ -14,12 +14,15 @@ process {
memory = { 6.GB * task.attempt }
time = { 4.h * task.attempt }
- errorStrategy = { task.exitStatus in ((130..145) + 104) ? 'retry' : 'finish' }
+ errorStrategy = { task.exitStatus in ((130..145) + 104 + 175) ? 'retry' : 'finish' }
maxRetries = 1
maxErrors = '-1'
// Process-specific resource requirements
- // See https://www.nextflow.io/docs/latest/config.html#config-process-selectors
+ // NOTE - Please try and reuse the labels below as much as possible.
+ // These labels are used and recognised by default in DSL2 files hosted on nf-core/modules.
+ // If possible, it would be nice to keep the same label naming convention when
+ // adding in your local modules too.
withLabel:error_ignore {
errorStrategy = 'ignore'
}
@@ -60,4 +63,8 @@ process {
errorStrategy = 'retry'
maxRetries = 2
}
+ withLabel: process_gpu {
+ ext.use_gpu = { workflow.profile.contains('gpu') }
+ accelerator = { workflow.profile.contains('gpu') ? 1 : null }
+ }
}
diff --git a/conf/test.config b/conf/test.config
index a205f58..7e254f2 100644
--- a/conf/test.config
+++ b/conf/test.config
@@ -23,7 +23,6 @@ params {
config_profile_description = 'Minimal test dataset to check pipeline function'
// Input data
-
input = "${projectDir}/tests/samplesheets/samplesheet.csv"
fasta = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/genome.fasta'
intervals = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/genome.bed'
diff --git a/docs/usage.md b/docs/usage.md
index 42c7011..cc352ba 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -186,7 +186,7 @@ If `-profile` is not specified, the pipeline will run locally and expect all sof
- `shifter`
- A generic configuration profile to be used with [Shifter](https://nersc.gitlab.io/development/shifter/how-to-use/)
- `charliecloud`
- - A generic configuration profile to be used with [Charliecloud](https://hpc.github.io/charliecloud/)
+ - A generic configuration profile to be used with [Charliecloud](https://charliecloud.io/)
- `apptainer`
- A generic configuration profile to be used with [Apptainer](https://apptainer.org/)
- `wave`
diff --git a/main.nf b/main.nf
index ee6651d..c32d5a6 100644
--- a/main.nf
+++ b/main.nf
@@ -92,7 +92,10 @@ workflow {
params.monochrome_logs,
args,
params.outdir,
- params.input
+ params.input,
+ params.help,
+ params.help_full,
+ params.show_hidden
)
//
diff --git a/modules.json b/modules.json
index 99212cf..925fac8 100644
--- a/modules.json
+++ b/modules.json
@@ -7,7 +7,7 @@
"nf-core": {
"bcftools/view": {
"branch": "master",
- "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
+ "git_sha": "81880787133db07d9b4c1febd152c090eb8325dc",
"installed_by": ["modules"]
},
"gunzip": {
@@ -17,29 +17,28 @@
},
"multiqc": {
"branch": "master",
- "git_sha": "f0719ae309075ae4a291533883847c3f7c441dad",
+ "git_sha": "dfa7f1a33781e89f6efe727d371ed7ca9077059d",
"installed_by": ["modules"]
},
"picard/liftovervcf": {
"branch": "master",
- "git_sha": "49f4e50534fe4b64101e62ea41d5dc43b1324358",
+ "git_sha": "81880787133db07d9b4c1febd152c090eb8325dc",
"installed_by": ["modules"]
},
"tabix/tabix": {
"branch": "master",
- "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
+ "git_sha": "7b972bdde6fa2154a95cf08a8ba1821f228f20d3",
"installed_by": ["modules"]
},
"untar": {
"branch": "master",
- "git_sha": "3e548877f25a5980a177cc4f81d2d2e8c24164ef",
+ "git_sha": "05954dab2ff481bcb999f24455da29a5828af08d",
"installed_by": ["modules"]
},
"vcf2maf": {
"branch": "master",
- "git_sha": "538cbd31deef6e6abe0daafa704a918ad6974699",
- "installed_by": ["modules"],
- "patch": "modules/nf-core/vcf2maf/vcf2maf.diff"
+ "git_sha": "81880787133db07d9b4c1febd152c090eb8325dc",
+ "installed_by": ["modules"]
}
}
},
@@ -47,17 +46,17 @@
"nf-core": {
"utils_nextflow_pipeline": {
"branch": "master",
- "git_sha": "c2b22d85f30a706a3073387f30380704fcae013b",
+ "git_sha": "05954dab2ff481bcb999f24455da29a5828af08d",
"installed_by": ["subworkflows"]
},
"utils_nfcore_pipeline": {
"branch": "master",
- "git_sha": "51ae5406a030d4da1e49e4dab49756844fdd6c7a",
+ "git_sha": "271e7fc14eb1320364416d996fb077421f3faed2",
"installed_by": ["subworkflows"]
},
"utils_nfschema_plugin": {
"branch": "master",
- "git_sha": "2fd2cd6d0e7b273747f32e465fdc6bcc3ae0814e",
+ "git_sha": "4b406a74dc0449c0401ed87d5bfff4252fd277fd",
"installed_by": ["subworkflows"]
}
}
diff --git a/modules/nf-core/multiqc/environment.yml b/modules/nf-core/multiqc/environment.yml
index a27122c..d02016a 100644
--- a/modules/nf-core/multiqc/environment.yml
+++ b/modules/nf-core/multiqc/environment.yml
@@ -1,5 +1,7 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
channels:
- conda-forge
- bioconda
dependencies:
- - bioconda::multiqc=1.27
+ - bioconda::multiqc=1.32
diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf
index 58d9313..82f8979 100644
--- a/modules/nf-core/multiqc/main.nf
+++ b/modules/nf-core/multiqc/main.nf
@@ -3,11 +3,11 @@ process MULTIQC {
conda "${moduleDir}/environment.yml"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
- 'https://depot.galaxyproject.org/singularity/multiqc:1.27--pyhdfd78af_0' :
- 'biocontainers/multiqc:1.27--pyhdfd78af_0' }"
+ 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/8c/8c6c120d559d7ee04c7442b61ad7cf5a9e8970be5feefb37d68eeaa60c1034eb/data' :
+ 'community.wave.seqera.io/library/multiqc:1.32--d58f60e4deb769bf' }"
input:
- path multiqc_files, stageAs: "?/*"
+ path multiqc_files, stageAs: "?/*"
path(multiqc_config)
path(extra_multiqc_config)
path(multiqc_logo)
@@ -15,10 +15,11 @@ process MULTIQC {
path(sample_names)
output:
- path "*multiqc_report.html", emit: report
- path "*_data" , emit: data
- path "*_plots" , optional:true, emit: plots
- path "versions.yml" , emit: versions
+ path "*.html" , emit: report
+ path "*_data" , emit: data
+ path "*_plots" , optional:true, emit: plots
+ tuple val("${task.process}"), val('multiqc'), eval('multiqc --version | sed "s/.* //g"'), emit: versions
+ // MultiQC should not push its versions to the `versions` topic. Its input depends on the versions topic to be resolved thus outputting to the topic will let the pipeline hang forever
when:
task.ext.when == null || task.ext.when
@@ -26,38 +27,29 @@ process MULTIQC {
script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ? "--filename ${task.ext.prefix}.html" : ''
- def config = multiqc_config ? "--config $multiqc_config" : ''
- def extra_config = extra_multiqc_config ? "--config $extra_multiqc_config" : ''
+ def config = multiqc_config ? "--config ${multiqc_config}" : ''
+ def extra_config = extra_multiqc_config ? "--config ${extra_multiqc_config}" : ''
def logo = multiqc_logo ? "--cl-config 'custom_logo: \"${multiqc_logo}\"'" : ''
def replace = replace_names ? "--replace-names ${replace_names}" : ''
def samples = sample_names ? "--sample-names ${sample_names}" : ''
"""
multiqc \\
--force \\
- $args \\
- $config \\
- $prefix \\
- $extra_config \\
- $logo \\
- $replace \\
- $samples \\
+ ${args} \\
+ ${config} \\
+ ${prefix} \\
+ ${extra_config} \\
+ ${logo} \\
+ ${replace} \\
+ ${samples} \\
.
-
- cat <<-END_VERSIONS > versions.yml
- "${task.process}":
- multiqc: \$( multiqc --version | sed -e "s/multiqc, version //g" )
- END_VERSIONS
"""
stub:
"""
mkdir multiqc_data
+ touch multiqc_data/.stub
mkdir multiqc_plots
touch multiqc_report.html
-
- cat <<-END_VERSIONS > versions.yml
- "${task.process}":
- multiqc: \$( multiqc --version | sed -e "s/multiqc, version //g" )
- END_VERSIONS
"""
}
diff --git a/modules/nf-core/multiqc/meta.yml b/modules/nf-core/multiqc/meta.yml
index b16c187..e4b8f94 100644
--- a/modules/nf-core/multiqc/meta.yml
+++ b/modules/nf-core/multiqc/meta.yml
@@ -15,57 +15,75 @@ tools:
licence: ["GPL-3.0-or-later"]
identifier: biotools:multiqc
input:
- - - multiqc_files:
- type: file
- description: |
- List of reports / files recognised by MultiQC, for example the html and zip output of FastQC
- - - multiqc_config:
- type: file
- description: Optional config yml for MultiQC
- pattern: "*.{yml,yaml}"
- - - extra_multiqc_config:
- type: file
- description: Second optional config yml for MultiQC. Will override common sections
- in multiqc_config.
- pattern: "*.{yml,yaml}"
- - - multiqc_logo:
- type: file
- description: Optional logo file for MultiQC
- pattern: "*.{png}"
- - - replace_names:
+ - multiqc_files:
+ type: file
+ description: |
+ List of reports / files recognised by MultiQC, for example the html and zip output of FastQC
+ ontologies: []
+ - multiqc_config:
+ type: file
+ description: Optional config yml for MultiQC
+ pattern: "*.{yml,yaml}"
+ ontologies:
+ - edam: http://edamontology.org/format_3750 # YAML
+ - extra_multiqc_config:
+ type: file
+ description: Second optional config yml for MultiQC. Will override common sections
+ in multiqc_config.
+ pattern: "*.{yml,yaml}"
+ ontologies:
+ - edam: http://edamontology.org/format_3750 # YAML
+ - multiqc_logo:
+ type: file
+ description: Optional logo file for MultiQC
+ pattern: "*.{png}"
+ ontologies: []
+ - replace_names:
+ type: file
+ description: |
+ Optional two-column sample renaming file. First column a set of
+ patterns, second column a set of corresponding replacements. Passed via
+ MultiQC's `--replace-names` option.
+ pattern: "*.{tsv}"
+ ontologies:
+ - edam: http://edamontology.org/format_3475 # TSV
+ - sample_names:
+ type: file
+ description: |
+ Optional TSV file with headers, passed to the MultiQC --sample_names
+ argument.
+ pattern: "*.{tsv}"
+ ontologies:
+ - edam: http://edamontology.org/format_3475 # TSV
+output:
+ report:
+ - "*.html":
type: file
- description: |
- Optional two-column sample renaming file. First column a set of
- patterns, second column a set of corresponding replacements. Passed via
- MultiQC's `--replace-names` option.
- pattern: "*.{tsv}"
- - - sample_names:
+ description: MultiQC report file
+ pattern: ".html"
+ ontologies: []
+ data:
+ - "*_data":
+ type: directory
+ description: MultiQC data dir
+ pattern: "multiqc_data"
+ plots:
+ - "*_plots":
type: file
- description: |
- Optional TSV file with headers, passed to the MultiQC --sample_names
- argument.
- pattern: "*.{tsv}"
-output:
- - report:
- - "*multiqc_report.html":
- type: file
- description: MultiQC report file
- pattern: "multiqc_report.html"
- - data:
- - "*_data":
- type: directory
- description: MultiQC data dir
- pattern: "multiqc_data"
- - plots:
- - "*_plots":
- type: file
- description: Plots created by MultiQC
- pattern: "*_data"
- - versions:
- - versions.yml:
- type: file
- description: File containing software versions
- pattern: "versions.yml"
+ description: Plots created by MultiQC
+ pattern: "*_data"
+ ontologies: []
+ versions:
+ - - ${task.process}:
+ type: string
+ description: The process the versions were collected from
+ - multiqc:
+ type: string
+ description: The tool name
+ - multiqc --version | sed "s/.* //g":
+ type: eval
+ description: The expression to obtain the version of the tool
+
authors:
- "@abhi18av"
- "@bunop"
diff --git a/modules/nf-core/multiqc/tests/custom_prefix.config b/modules/nf-core/multiqc/tests/custom_prefix.config
new file mode 100644
index 0000000..b30b135
--- /dev/null
+++ b/modules/nf-core/multiqc/tests/custom_prefix.config
@@ -0,0 +1,5 @@
+process {
+ withName: 'MULTIQC' {
+ ext.prefix = "custom_prefix"
+ }
+}
diff --git a/modules/nf-core/multiqc/tests/main.nf.test b/modules/nf-core/multiqc/tests/main.nf.test
index 33316a7..d1ae8b0 100644
--- a/modules/nf-core/multiqc/tests/main.nf.test
+++ b/modules/nf-core/multiqc/tests/main.nf.test
@@ -30,7 +30,33 @@ nextflow_process {
{ assert process.success },
{ assert process.out.report[0] ==~ ".*/multiqc_report.html" },
{ assert process.out.data[0] ==~ ".*/multiqc_data" },
- { assert snapshot(process.out.versions).match("multiqc_versions_single") }
+ { assert snapshot(process.out.findAll { key, val -> key.startsWith("versions")}).match() }
+ )
+ }
+
+ }
+
+ test("sarscov2 single-end [fastqc] - custom prefix") {
+ config "./custom_prefix.config"
+
+ when {
+ process {
+ """
+ input[0] = Channel.of(file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastqc/test_fastqc.zip', checkIfExists: true))
+ input[1] = []
+ input[2] = []
+ input[3] = []
+ input[4] = []
+ input[5] = []
+ """
+ }
+ }
+
+ then {
+ assertAll(
+ { assert process.success },
+ { assert process.out.report[0] ==~ ".*/custom_prefix.html" },
+ { assert process.out.data[0] ==~ ".*/custom_prefix_data" }
)
}
@@ -56,7 +82,7 @@ nextflow_process {
{ assert process.success },
{ assert process.out.report[0] ==~ ".*/multiqc_report.html" },
{ assert process.out.data[0] ==~ ".*/multiqc_data" },
- { assert snapshot(process.out.versions).match("multiqc_versions_config") }
+ { assert snapshot(process.out.findAll { key, val -> key.startsWith("versions")}).match() }
)
}
}
@@ -84,7 +110,7 @@ nextflow_process {
{ assert snapshot(process.out.report.collect { file(it).getName() } +
process.out.data.collect { file(it).getName() } +
process.out.plots.collect { file(it).getName() } +
- process.out.versions ).match("multiqc_stub") }
+ process.out.findAll { key, val -> key.startsWith("versions")} ).match() }
)
}
diff --git a/modules/nf-core/multiqc/tests/main.nf.test.snap b/modules/nf-core/multiqc/tests/main.nf.test.snap
index 7b7c132..3a8ce6b 100644
--- a/modules/nf-core/multiqc/tests/main.nf.test.snap
+++ b/modules/nf-core/multiqc/tests/main.nf.test.snap
@@ -1,41 +1,61 @@
{
- "multiqc_versions_single": {
+ "sarscov2 single-end [fastqc]": {
"content": [
- [
- "versions.yml:md5,8f3b8c1cec5388cf2708be948c9fa42f"
- ]
+ {
+ "versions": [
+ [
+ "MULTIQC",
+ "multiqc",
+ "1.32"
+ ]
+ ]
+ }
],
"meta": {
"nf-test": "0.9.2",
- "nextflow": "24.10.4"
+ "nextflow": "25.04.6"
},
- "timestamp": "2025-01-27T09:29:57.631982377"
+ "timestamp": "2025-12-09T10:10:43.020315838"
},
- "multiqc_stub": {
+ "sarscov2 single-end [fastqc] - stub": {
"content": [
[
"multiqc_report.html",
"multiqc_data",
"multiqc_plots",
- "versions.yml:md5,8f3b8c1cec5388cf2708be948c9fa42f"
+ {
+ "versions": [
+ [
+ "MULTIQC",
+ "multiqc",
+ "1.32"
+ ]
+ ]
+ }
]
],
"meta": {
"nf-test": "0.9.2",
- "nextflow": "24.10.4"
+ "nextflow": "25.04.6"
},
- "timestamp": "2025-01-27T09:30:34.743726958"
+ "timestamp": "2025-12-09T10:11:14.131950776"
},
- "multiqc_versions_config": {
+ "sarscov2 single-end [fastqc] [config]": {
"content": [
- [
- "versions.yml:md5,8f3b8c1cec5388cf2708be948c9fa42f"
- ]
+ {
+ "versions": [
+ [
+ "MULTIQC",
+ "multiqc",
+ "1.32"
+ ]
+ ]
+ }
],
"meta": {
"nf-test": "0.9.2",
- "nextflow": "24.10.4"
+ "nextflow": "25.04.6"
},
- "timestamp": "2025-01-27T09:30:21.44383553"
+ "timestamp": "2025-12-09T10:11:07.15692209"
}
}
\ No newline at end of file
diff --git a/modules/nf-core/multiqc/tests/tags.yml b/modules/nf-core/multiqc/tests/tags.yml
deleted file mode 100644
index bea6c0d..0000000
--- a/modules/nf-core/multiqc/tests/tags.yml
+++ /dev/null
@@ -1,2 +0,0 @@
-multiqc:
- - modules/nf-core/multiqc/**
diff --git a/modules/nf-core/picard/liftovervcf/environment.yml b/modules/nf-core/picard/liftovervcf/environment.yml
index 1d715d5..fb68506 100644
--- a/modules/nf-core/picard/liftovervcf/environment.yml
+++ b/modules/nf-core/picard/liftovervcf/environment.yml
@@ -2,4 +2,4 @@ channels:
- conda-forge
- bioconda
dependencies:
- - bioconda::picard=3.3.0
+ - bioconda::picard=3.3.0
\ No newline at end of file
diff --git a/nextflow.config b/nextflow.config
index 19f6d00..8ab40c0 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -36,13 +36,15 @@ params {
email_on_fail = null
plaintext_email = false
monochrome_logs = false
- hook_url = null
+ hook_url = System.getenv('HOOK_URL')
help = false
help_full = false
show_hidden = false
version = false
pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/'
- trace_report_suffix = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')// Config options
+ trace_report_suffix = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')
+
+ // Config options
config_profile_name = null
config_profile_description = null
@@ -96,7 +98,18 @@ profiles {
apptainer.enabled = false
docker.runOptions = '-u $(id -u):$(id -g)'
}
- arm {
+ arm64 {
+ process.arch = 'arm64'
+ // TODO https://github.com/nf-core/modules/issues/6694
+ // For now if you're using arm64 you have to use wave for the sake of the maintainers
+ // wave profile
+ apptainer.ociAutoPull = true
+ singularity.ociAutoPull = true
+ wave.enabled = true
+ wave.freeze = true
+ wave.strategy = 'conda,container'
+ }
+ emulate_amd64 {
docker.runOptions = '-u $(id -u):$(id -g) --platform=linux/amd64'
}
singularity {
@@ -153,31 +166,25 @@ profiles {
wave.freeze = true
wave.strategy = 'conda,container'
}
- gitpod {
- executor.name = 'local'
- executor.cpus = 4
- executor.memory = 8.GB
- process {
- resourceLimits = [
- memory: 8.GB,
- cpus : 4,
- time : 1.h
- ]
- }
+ gpu {
+ docker.runOptions = '-u $(id -u):$(id -g) --gpus all'
+ apptainer.runOptions = '--nv'
+ singularity.runOptions = '--nv'
}
- test { includeConfig 'conf/test.config' }
- test_vep { includeConfig 'conf/test_vep.config' }
+ test { includeConfig 'conf/test.config' }
}
+// Set default registry for Apptainer, Docker, Podman, Charliecloud and Singularity independent of -profile
+// Will not be used unless Apptainer / Docker / Podman / Charliecloud / Singularity are enabled
+// Set to your registry if you have a mirror of containers
apptainer.registry = 'quay.io'
docker.registry = 'quay.io'
podman.registry = 'quay.io'
singularity.registry = 'quay.io'
charliecloud.registry = 'quay.io'
-// Load nf-core custom profiles from different Institutions
-includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/nfcore_custom.config" : "/dev/null"
-
+// Load nf-core custom profiles from different institutions │
+includeConfig params.custom_config_base && (!System.getenv('NXF_OFFLINE') || !params.custom_config_base.startsWith('http')) ? "${params.custom_config_base}/nfcore_custom.config" : "/dev/null"
// Load igenomes.config if required
includeConfig !params.igenomes_ignore ? 'conf/igenomes.config' : 'conf/igenomes_ignored.config'
@@ -185,7 +192,6 @@ includeConfig !params.igenomes_ignore ? 'conf/igenomes.config' : 'conf/igenomes_
// Export these variables to prevent local Python/R libraries from conflicting with those in the container
// The JULIA depot path has been adjusted to a fixed path `/usr/local/share/julia` that needs to be used for packages in the container.
// See https://apeltzer.github.io/post/03-julia-lang-nextflow/ for details on that. Once we have a common agreement on where to keep Julia packages, this is adjustable.
-
env {
PYTHONNOUSERSITE = 1
R_PROFILE_USER = "/.Rprofile"
@@ -225,46 +231,44 @@ dag {
manifest {
name = 'qbic-pipelines/vcftomaf'
- author = """SusiJo, FriederikeHanssen, famosab""" // The author field is deprecated from Nextflow version 24.10.0, use contributors instead
contributors = [
- // TODO nf-core: Update the field with the details of the contributors to your pipeline. New with Nextflow version 24.10.0
[
- name: 'SusiJo',
- affiliation: '',
+ name: 'Susanne Jodoin',
+ affiliation: 'Quantitative Biology Center (QBiC) Tübingen, University of Tübingen, Germany',
email: '',
- github: '',
- contribution: [], // List of contribution types ('author', 'maintainer' or 'contributor')
- orcid: ''
+ github: '@SusiJo',
+ contribution: ['author'],
+ orcid: '0009-0001-9152-7291'
],
[
- name: ' FriederikeHanssen',
- affiliation: '',
+ name: 'Friederike Hanssen',
+ affiliation: 'Seqera',
email: '',
- github: '',
- contribution: [], // List of contribution types ('author', 'maintainer' or 'contributor')
- orcid: ''
+ github: '@FriederikeHanssen',
+ contribution: ['author'],
+ orcid: '0009-0001-9875-5262'
],
[
- name: ' famosab',
- affiliation: '',
- email: '',
- github: '',
- contribution: [], // List of contribution types ('author', 'maintainer' or 'contributor')
- orcid: ''
- ],
+ name: 'Famke Bäuerle',
+ affiliation: 'Quantitative Biology Center (QBiC) Tübingen, University of Tübingen, Germany',
+ email: 'famke.baeuerle@uni-tuebingen.de',
+ github: '@famosab',
+ contribution: ['maintainer'],
+ orcid: '0000-0003-1387-0251'
+ ]
]
homePage = 'https://github.com/qbic-pipelines/vcftomaf'
description = """Convert vcf files to maf format"""
mainScript = 'main.nf'
defaultBranch = 'master'
- nextflowVersion = '!>=24.04.2'
+ nextflowVersion = '!>=25.04.0'
version = '1.3.0dev'
doi = '10.5281/zenodo.10812762'
}
// Nextflow plugins
plugins {
- id 'nf-schema@2.2.0' // Validation of pipeline parameters and creation of an input channel from a sample sheet
+ id 'nf-schema@2.5.1' // Validation of pipeline parameters and creation of an input channel from a sample sheet
}
validation {
diff --git a/nextflow_schema.json b/nextflow_schema.json
index 0c1f772..460d3e3 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -258,6 +258,18 @@
"fa_icon": "far calendar",
"description": "Suffix to add to the trace report filename. Default is the date and time in the format yyyy-MM-dd_HH-mm-ss.",
"hidden": true
+ },
+ "help": {
+ "type": ["boolean", "string"],
+ "description": "Display the help message."
+ },
+ "help_full": {
+ "type": "boolean",
+ "description": "Display the full detailed help message."
+ },
+ "show_hidden": {
+ "type": "boolean",
+ "description": "Display hidden parameters in the help message (only works when --help or --help_full are provided)."
}
}
}
diff --git a/nf-test.config b/nf-test.config
index be70ff0..4d13419 100644
--- a/nf-test.config
+++ b/nf-test.config
@@ -9,7 +9,7 @@ config {
configFile "tests/nextflow.config"
// ignore tests coming from the nf-core/modules repo
- ignore 'modules/nf-core/**/*', 'subworkflows/nf-core/**/*'
+ ignore 'modules/nf-core/**/tests/*', 'subworkflows/nf-core/**/tests/*'
// run all test with defined profile(s) from the main nextflow.config
profile "test"
diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json
index 661f5d7..b136d52 100644
--- a/ro-crate-metadata.json
+++ b/ro-crate-metadata.json
@@ -23,7 +23,7 @@
"@type": "Dataset",
"creativeWorkStatus": "InProgress",
"datePublished": "2025-01-15T13:46:40+00:00",
- "description": "#  \n\n[](https://github.com/qbic-pipelines/vcftomaf/actions/workflows/ci.yml)\n[](https://github.com/qbic-pipelines/vcftomaf/actions/workflows/linting.yml)[](https://doi.org/10.5281/zenodo.10812762)\n[](https://www.nf-test.com)\n\n[](https://www.nextflow.io/)\n[](https://docs.conda.io/en/latest/)\n[](https://www.docker.com/)\n[](https://sylabs.io/docs/)\n[](https://tower.nf/launch?pipeline=https://github.com/qbic-pipelines/vcftomaf)\n\n## Introduction\n\n**qbic-pipelines/vcftomaf** is a bioinformatics pipeline that converts input Variant Call Format (vcf) files with one or two columns of (paired) samples to tabular Mutation Annotation Format (maf).\nThe resulting file(s) can be analyzed singly or as an entire cohort in R with [maftools](https://github.com/PoisonAlien/maftools).\n\n\n ![](\"docs/images/metromap.png\" "\\"Overview\\"")
\n
\n\n1. Optional Filtering of VCF files for PASS and / or with a target bed file ([`BCFtools`](https://github.com/samtools/bcftools))\n2. Optional liftover (needs a `chain` file, `--fasta` should refer to target genome version) ([`Picard LiftOverVCF`](https://gatk.broadinstitute.org/hc/en-us/articles/360037060932-LiftoverVcf-Picard))\n3. Conversion from vcf to maf format([`vcf2maf`](https://github.com/mskcc/vcf2maf))\n4. Collect QC metrics and versions ([`MultiQC`](http://multiqc.info/))\n\n## Usage\n\n> [!NOTE]\n> 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.\n\nFirst, prepare a samplesheet with your input data that looks as follows:\n\n`samplesheet.csv`:\n\n```csv\nsample,normal_id,vcf_normal_id,tumor_id,vcf_tumor_id,vcf,index\nmutect2_sample1,SAMPLE123,PATIENT1_SAMPLE123,SAMPLE456,PATIENT1_SAMPLE456,/path/to/vcf,/path/to/tbi\ntest2,control2,NORMAl,,,/path/to/vcf,/path/to/tbi\n```\n\nEach row represents a sample with one or two columns in the VCF file. The `normal_id` and `tumor_id` will be used for naming the columns in the MAF file. The `vcf_normal/tumor_id` refers to the sample name in the VCF file. This differs for each caller. For VCFs obtained from nf-core/sarek, the following is tested:\n\n| Caller | Normal ID | Tumor ID |\n| :------- | :---------------------- | :---------------------- |\n| Manta | NORMAL | TUMOR |\n| Mutect2 | {_patient_}_{\\_sample_} | {_patient_}_{\\_sample_} |\n| Strelka2 | NORMAL | TUMOR |\n\nThe values for _patient_ and _sample_ can be obtained from the nf-core/sarek samplesheet.\n\nNow, you can run the pipeline using:\n\n```bash\nnextflow run qbic-pipelines/vcftomaf \\\n -profile \\\n --input samplesheet.csv \\\n --outdir \n```\n\n> [!WARNING]\n> 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**_;\n> see [docs](https://nf-co.re/usage/configuration#custom-configuration-files).\n\nFor more details and further functionality, please refer to the [usage documentation](docs/usage.md) and the [parameter documentation](nextflow_schema.json).\n\nFor more details about the output files and reports, please refer to the\n[output documentation](docs/output.md).\n\n## Credits\n\nqbic-pipelines/vcftomaf was originally written by [SusiJo](https://github.com/SusiJo), [Friederike Hanssen](https://github.com/FriederikeHanssen) up to release 1.0.0. The pipeline was further developed by [Famke B\u00e4uerle](https://github.com/famosab) after release 1.0.0.\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).\n\n## Citations\n\nIf you use qbic-pipelines/vcftomaf for your analysis, please cite it using the following doi: [10.5281/zenodo.10812762](https://zenodo.org/doi/10.5281/zenodo.10812762)\n\n\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nThis pipeline is based on code and infrastructure developed and maintained by the [nf-core](https://nf-co.re) community, reused here under the [MIT license](https://github.com/nf-core/tools/blob/master/LICENSE).\nThe pipeline is currently maintained at QBiC and not an nf-core pipeline since it has not undergone nf-core community review.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n",
+ "description": "#  \n\n[](https://github.com/codespaces/new/qbic-pipelines/vcftomaf)\n[](https://github.com/qbic-pipelines/vcftomaf/actions/workflows/nf-test.yml)\n[](https://github.com/qbic-pipelines/vcftomaf/actions/workflows/linting.yml)[](https://doi.org/10.5281/zenodo.10812762)\n[](https://www.nf-test.com)\n\n[](https://www.nextflow.io/)\n[](https://github.com/nf-core/tools/releases/tag/3.5.1)\n[](https://docs.conda.io/en/latest/)\n[](https://www.docker.com/)\n[](https://sylabs.io/docs/)\n[](https://tower.nf/launch?pipeline=https://github.com/qbic-pipelines/vcftomaf)\n\n## Introduction\n\n**qbic-pipelines/vcftomaf** is a bioinformatics pipeline that converts input Variant Call Format (vcf) files with one or two columns of (paired) samples to tabular Mutation Annotation Format (maf).\nThe resulting file(s) can be analyzed singly or as an entire cohort in R with [maftools](https://github.com/PoisonAlien/maftools).\n\n\n \n
\n\n1. Optional Filtering of VCF files for PASS and / or with a target bed file ([`BCFtools`](https://github.com/samtools/bcftools))\n2. Optional liftover (needs a `chain` file, `--fasta` should refer to target genome version) ([`Picard LiftOverVCF`](https://gatk.broadinstitute.org/hc/en-us/articles/360037060932-LiftoverVcf-Picard))\n3. Conversion from vcf to maf format([`vcf2maf`](https://github.com/mskcc/vcf2maf))\n4. Collect QC metrics and versions ([`MultiQC`](http://multiqc.info/))\n\n## Usage\n\n> [!NOTE]\n> 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.\n\nFirst, prepare a samplesheet with your input data that looks as follows:\n\n`samplesheet.csv`:\n\n```csv\nsample,normal_id,vcf_normal_id,tumor_id,vcf_tumor_id,vcf,index\nmutect2_sample1,SAMPLE123,PATIENT1_SAMPLE123,SAMPLE456,PATIENT1_SAMPLE456,/path/to/vcf,/path/to/tbi\ntest2,control2,NORMAl,,,/path/to/vcf,/path/to/tbi\n```\n\nEach row represents a sample with one or two columns in the VCF file. The `normal_id` and `tumor_id` will be used for naming the columns in the MAF file. The `vcf_normal/tumor_id` refers to the sample name in the VCF file. This differs for each caller. For VCFs obtained from nf-core/sarek, the following is tested:\n\n| Caller | Normal ID | Tumor ID |\n| :------- | :---------------------- | :---------------------- |\n| Manta | NORMAL | TUMOR |\n| Mutect2 | {_patient_}_{\\_sample_} | {_patient_}_{\\_sample_} |\n| Strelka2 | NORMAL | TUMOR |\n\nThe values for _patient_ and _sample_ can be obtained from the nf-core/sarek samplesheet.\n\nNow, you can run the pipeline using:\n\n```bash\nnextflow run qbic-pipelines/vcftomaf \\\n -profile \\\n --input samplesheet.csv \\\n --outdir \n```\n\n> [!WARNING]\n> 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**_;\n> see [docs](https://nf-co.re/usage/configuration#custom-configuration-files).\n\nFor more details and further functionality, please refer to the [usage documentation](docs/usage.md) and the [parameter documentation](nextflow_schema.json).\n\nFor more details about the output files and reports, please refer to the\n[output documentation](docs/output.md).\n\n## Credits\n\nqbic-pipelines/vcftomaf was originally written by [SusiJo](https://github.com/SusiJo), [Friederike Hanssen](https://github.com/FriederikeHanssen) up to release 1.0.0. The pipeline was further developed by [Famke B\u00e4uerle](https://github.com/famosab) after release 1.0.0.\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).\n\n## Citations\n\nIf you use qbic-pipelines/vcftomaf for your analysis, please cite it using the following doi: [10.5281/zenodo.10812762](https://zenodo.org/doi/10.5281/zenodo.10812762)\n\n\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nThis pipeline is based on code and infrastructure developed and maintained by the [nf-core](https://nf-co.re) community, reused here under the [MIT license](https://github.com/nf-core/tools/blob/master/LICENSE).\nThe pipeline is currently maintained at QBiC and not an nf-core pipeline since it has not undergone nf-core community review.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n",
"hasPart": [
{
"@id": "main.nf"
diff --git a/subworkflows/local/utils_nfcore_vcftomaf_pipeline/main.nf b/subworkflows/local/utils_nfcore_vcftomaf_pipeline/main.nf
index ad4e498..def884d 100644
--- a/subworkflows/local/utils_nfcore_vcftomaf_pipeline/main.nf
+++ b/subworkflows/local/utils_nfcore_vcftomaf_pipeline/main.nf
@@ -11,6 +11,7 @@
include { UTILS_NFSCHEMA_PLUGIN } from '../../nf-core/utils_nfschema_plugin'
include { paramsSummaryMap } from 'plugin/nf-schema'
include { samplesheetToList } from 'plugin/nf-schema'
+include { paramsHelp } from 'plugin/nf-schema'
include { completionEmail } from '../../nf-core/utils_nfcore_pipeline'
include { completionSummary } from '../../nf-core/utils_nfcore_pipeline'
include { imNotification } from '../../nf-core/utils_nfcore_pipeline'
@@ -32,10 +33,13 @@ workflow PIPELINE_INITIALISATION {
nextflow_cli_args // array: List of positional nextflow CLI args
outdir // string: The output directory where the results will be saved
input // string: Path to input samplesheet
+ help // boolean: Display help message and exit
+ help_full // boolean: Show the full help message
+ show_hidden // boolean: Show hidden parameters in the help message
main:
- ch_versions = Channel.empty()
+ ch_versions = channel.empty()
//
// Print version and exit if required and dump pipeline parameters to JSON file
@@ -50,10 +54,18 @@ workflow PIPELINE_INITIALISATION {
//
// Validate parameters and generate parameter summary to stdout
//
+ command = "nextflow run ${workflow.manifest.name} -profile --input samplesheet.csv --outdir "
+
UTILS_NFSCHEMA_PLUGIN (
workflow,
validate_params,
- null
+ null,
+ help,
+ help_full,
+ show_hidden,
+ "",
+ "",
+ command
)
//
@@ -254,4 +266,3 @@ def methodsDescriptionText(mqc_methods_yaml) {
return description_html.toString()
}
-
diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/tags.yml b/subworkflows/nf-core/utils_nextflow_pipeline/tests/tags.yml
deleted file mode 100644
index f847611..0000000
--- a/subworkflows/nf-core/utils_nextflow_pipeline/tests/tags.yml
+++ /dev/null
@@ -1,2 +0,0 @@
-subworkflows/utils_nextflow_pipeline:
- - subworkflows/nf-core/utils_nextflow_pipeline/**
diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf
index bfd2587..2f30e9a 100644
--- a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf
+++ b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf
@@ -98,7 +98,7 @@ def workflowVersionToYAML() {
// Get channel of software versions used in pipeline in YAML format
//
def softwareVersionsToYAML(ch_versions) {
- return ch_versions.unique().map { version -> processVersionsFromYAML(version) }.unique().mix(Channel.of(workflowVersionToYAML()))
+ return ch_versions.unique().map { version -> processVersionsFromYAML(version) }.unique().mix(channel.of(workflowVersionToYAML()))
}
//
diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/tags.yml b/subworkflows/nf-core/utils_nfcore_pipeline/tests/tags.yml
deleted file mode 100644
index ac8523c..0000000
--- a/subworkflows/nf-core/utils_nfcore_pipeline/tests/tags.yml
+++ /dev/null
@@ -1,2 +0,0 @@
-subworkflows/utils_nfcore_pipeline:
- - subworkflows/nf-core/utils_nfcore_pipeline/**
diff --git a/subworkflows/nf-core/utils_nfschema_plugin/main.nf b/subworkflows/nf-core/utils_nfschema_plugin/main.nf
index 4994303..ee4738c 100644
--- a/subworkflows/nf-core/utils_nfschema_plugin/main.nf
+++ b/subworkflows/nf-core/utils_nfschema_plugin/main.nf
@@ -4,6 +4,7 @@
include { paramsSummaryLog } from 'plugin/nf-schema'
include { validateParameters } from 'plugin/nf-schema'
+include { paramsHelp } from 'plugin/nf-schema'
workflow UTILS_NFSCHEMA_PLUGIN {
@@ -15,29 +16,56 @@ workflow UTILS_NFSCHEMA_PLUGIN {
// when this input is empty it will automatically use the configured schema or
// "${projectDir}/nextflow_schema.json" as default. This input should not be empty
// for meta pipelines
+ help // boolean: show help message
+ help_full // boolean: show full help message
+ show_hidden // boolean: show hidden parameters in help message
+ before_text // string: text to show before the help message and parameters summary
+ after_text // string: text to show after the help message and parameters summary
+ command // string: an example command of the pipeline
main:
+ if(help || help_full) {
+ help_options = [
+ beforeText: before_text,
+ afterText: after_text,
+ command: command,
+ showHidden: show_hidden,
+ fullHelp: help_full,
+ ]
+ if(parameters_schema) {
+ help_options << [parametersSchema: parameters_schema]
+ }
+ log.info paramsHelp(
+ help_options,
+ params.help instanceof String ? params.help : "",
+ )
+ exit 0
+ }
+
//
// Print parameter summary to stdout. This will display the parameters
// that differ from the default given in the JSON schema
//
+
+ summary_options = [:]
if(parameters_schema) {
- log.info paramsSummaryLog(input_workflow, parameters_schema:parameters_schema)
- } else {
- log.info paramsSummaryLog(input_workflow)
+ summary_options << [parametersSchema: parameters_schema]
}
+ log.info before_text
+ log.info paramsSummaryLog(summary_options, input_workflow)
+ log.info after_text
//
// Validate the parameters using nextflow_schema.json or the schema
// given via the validation.parametersSchema configuration option
//
if(validate_params) {
+ validateOptions = [:]
if(parameters_schema) {
- validateParameters(parameters_schema:parameters_schema)
- } else {
- validateParameters()
+ validateOptions << [parametersSchema: parameters_schema]
}
+ validateParameters(validateOptions)
}
emit:
diff --git a/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test b/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test
index 8fb3016..c977917 100644
--- a/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test
+++ b/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test
@@ -25,6 +25,12 @@ nextflow_workflow {
input[0] = workflow
input[1] = validate_params
input[2] = ""
+ input[3] = false
+ input[4] = false
+ input[5] = false
+ input[6] = ""
+ input[7] = ""
+ input[8] = ""
"""
}
}
@@ -51,6 +57,12 @@ nextflow_workflow {
input[0] = workflow
input[1] = validate_params
input[2] = ""
+ input[3] = false
+ input[4] = false
+ input[5] = false
+ input[6] = ""
+ input[7] = ""
+ input[8] = ""
"""
}
}
@@ -77,6 +89,12 @@ nextflow_workflow {
input[0] = workflow
input[1] = validate_params
input[2] = "${projectDir}/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json"
+ input[3] = false
+ input[4] = false
+ input[5] = false
+ input[6] = ""
+ input[7] = ""
+ input[8] = ""
"""
}
}
@@ -103,6 +121,12 @@ nextflow_workflow {
input[0] = workflow
input[1] = validate_params
input[2] = "${projectDir}/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json"
+ input[3] = false
+ input[4] = false
+ input[5] = false
+ input[6] = ""
+ input[7] = ""
+ input[8] = ""
"""
}
}
@@ -114,4 +138,36 @@ nextflow_workflow {
)
}
}
+
+ test("Should create a help message") {
+
+ when {
+
+ params {
+ test_data = ''
+ outdir = null
+ }
+
+ workflow {
+ """
+ validate_params = true
+ input[0] = workflow
+ input[1] = validate_params
+ input[2] = "${projectDir}/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json"
+ input[3] = true
+ input[4] = false
+ input[5] = false
+ input[6] = "Before"
+ input[7] = "After"
+ input[8] = "nextflow run test/test"
+ """
+ }
+ }
+
+ then {
+ assertAll(
+ { assert workflow.success }
+ )
+ }
+ }
}
diff --git a/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config b/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config
index 0907ac5..8d8c737 100644
--- a/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config
+++ b/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config
@@ -1,8 +1,8 @@
plugins {
- id "nf-schema@2.1.0"
+ id "nf-schema@2.5.1"
}
validation {
parametersSchema = "${projectDir}/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json"
monochromeLogs = true
-}
\ No newline at end of file
+}
diff --git a/tests/.nftignore b/tests/.nftignore
index 604d3ea..0b04f24 100644
--- a/tests/.nftignore
+++ b/tests/.nftignore
@@ -1,15 +1,12 @@
.DS_Store
csv/*.csv
fastqc/*_fastqc.{html,zip}
+multiqc/multiqc_data/multiqc.parquet
multiqc/multiqc_data/multiqc.log
-multiqc/multiqc_data/multiqc_bcftools_stats.txt
multiqc/multiqc_data/multiqc_data.json
-multiqc/multiqc_data/multiqc_general_stats.txt
-multiqc/multiqc_data/multiqc_picard_dups.txt
-multiqc/multiqc_data/multiqc_software_versions.txt
multiqc/multiqc_data/multiqc_sources.txt
-multiqc/multiqc_data/picard_deduplication.txt
-multiqc/multiqc_data/vcftools*.txt
+multiqc/multiqc_data/multiqc_software_versions.txt
+multiqc/multiqc_data/llms-full.txt
multiqc/multiqc_plots/{svg,pdf,png}/*.{svg,pdf,png}
multiqc/multiqc_report.html
pipeline_info/*.{html,json,txt,yml}
diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap
index 4356abf..1ce02bc 100644
--- a/tests/default.nf.test.snap
+++ b/tests/default.nf.test.snap
@@ -28,7 +28,9 @@
"maf/test2.maf",
"multiqc",
"multiqc/multiqc_data",
+ "multiqc/multiqc_data/llms-full.txt",
"multiqc/multiqc_data/multiqc.log",
+ "multiqc/multiqc_data/multiqc.parquet",
"multiqc/multiqc_data/multiqc_citations.txt",
"multiqc/multiqc_data/multiqc_data.json",
"multiqc/multiqc_data/multiqc_software_versions.txt",
diff --git a/tests/nextflow.config b/tests/nextflow.config
index 393cbed..58b39ec 100644
--- a/tests/nextflow.config
+++ b/tests/nextflow.config
@@ -11,5 +11,8 @@
aws.client.anonymous = true
// Should take care of all basepath
-params.modules_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/'
-params.igenomes_base = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data'
+params {
+ modules_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/'
+ igenomes_base = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data'
+ pipelines_testdata_base_path = 'https://github.com/qbic-pipelines/test-datasets/raw/refs/heads/main/'
+}
diff --git a/tests/vep.nf.test.snap b/tests/vep.nf.test.snap
index 852b855..3fcee3d 100644
--- a/tests/vep.nf.test.snap
+++ b/tests/vep.nf.test.snap
@@ -32,7 +32,9 @@
"maf/test2.maf",
"multiqc",
"multiqc/multiqc_data",
+ "multiqc/multiqc_data/llms-full.txt",
"multiqc/multiqc_data/multiqc.log",
+ "multiqc/multiqc_data/multiqc.parquet",
"multiqc/multiqc_data/multiqc_citations.txt",
"multiqc/multiqc_data/multiqc_data.json",
"multiqc/multiqc_data/multiqc_software_versions.txt",
diff --git a/workflows/vcftomaf/main.nf b/workflows/vcftomaf/main.nf
index 342f035..f5536a9 100644
--- a/workflows/vcftomaf/main.nf
+++ b/workflows/vcftomaf/main.nf
@@ -40,8 +40,8 @@ workflow VCFTOMAF {
main:
- ch_versions = Channel.empty()
- ch_multiqc_files = Channel.empty()
+ ch_versions = channel.empty()
+ ch_multiqc_files = channel.empty()
//
// SUBWORKFLOW: Read in samplesheet, validate and stage input files
@@ -121,20 +121,43 @@ workflow VCFTOMAF {
//
// Collate and save software versions
//
- softwareVersionsToYAML(ch_versions)
- .collectFile(storeDir: "${params.outdir}/pipeline_info", name: 'nf_core_pipeline_software_mqc_versions.yml', sort: true, newLine: true)
+ def topic_versions = channel.topic("versions")
+ .distinct()
+ .branch { entry ->
+ versions_file: entry instanceof Path
+ versions_tuple: true
+ }
+
+ def topic_versions_string = topic_versions.versions_tuple
+ .map { process, tool, version ->
+ [process[process.lastIndexOf(':') + 1..-1], " ${tool}: ${version}"]
+ }
+ .groupTuple(by: 0)
+ .map { process, tool_versions ->
+ tool_versions.unique().sort()
+ "${process}:\n${tool_versions.join('\n')}"
+ }
+
+ softwareVersionsToYAML(ch_versions.mix(topic_versions.versions_file))
+ .mix(topic_versions_string)
+ .collectFile(
+ storeDir: "${params.outdir}/pipeline_info",
+ name: 'nf_core_' + 'pipeline_software_' + 'mqc_' + 'versions.yml',
+ sort: true,
+ newLine: true,
+ )
.set { ch_collated_versions }
//
// MODULE: MultiQC
//
- ch_multiqc_config = Channel.fromPath("$projectDir/assets/multiqc_config.yml", checkIfExists: true)
- ch_multiqc_custom_config = params.multiqc_config ? Channel.fromPath(params.multiqc_config, checkIfExists: true) : Channel.empty()
- ch_multiqc_logo = params.multiqc_logo ? Channel.fromPath(params.multiqc_logo, checkIfExists: true) : Channel.empty()
+ ch_multiqc_config = channel.fromPath("$projectDir/assets/multiqc_config.yml", checkIfExists: true)
+ ch_multiqc_custom_config = params.multiqc_config ? channel.fromPath(params.multiqc_config, checkIfExists: true) : channel.empty()
+ ch_multiqc_logo = params.multiqc_logo ? channel.fromPath(params.multiqc_logo, checkIfExists: true) : channel.empty()
summary_params = paramsSummaryMap(workflow, parameters_schema: "nextflow_schema.json")
- ch_workflow_summary = Channel.value(paramsSummaryMultiqc(summary_params))
+ ch_workflow_summary = channel.value(paramsSummaryMultiqc(summary_params))
ch_multiqc_custom_methods_description = params.multiqc_methods_description ? file(params.multiqc_methods_description, checkIfExists: true) : file("$projectDir/assets/methods_description_template.yml", checkIfExists: true)
- ch_methods_description = Channel.value(methodsDescriptionText(ch_multiqc_custom_methods_description))
+ ch_methods_description = channel.value(methodsDescriptionText(ch_multiqc_custom_methods_description))
ch_multiqc_files = ch_multiqc_files.mix(ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml'))
ch_multiqc_files = ch_multiqc_files.mix(ch_collated_versions)
ch_multiqc_files = ch_multiqc_files.mix(ch_methods_description.collectFile(name: 'methods_description_mqc.yaml', sort: false))