diff --git a/.editorconfig b/.editorconfig
deleted file mode 100644
index 6d9b74cc..00000000
--- 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 9e279bc4..8b4772c2 100644
--- a/.github/CONTRIBUTING.md
+++ b/.github/CONTRIBUTING.md
@@ -82,7 +82,7 @@ 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
new file mode 100644
index 00000000..34085279
--- /dev/null
+++ b/.github/actions/get-shards/action.yml
@@ -0,0 +1,69 @@
+name: "Get number of shards"
+description: "Get the number of nf-test shards for the current CI job"
+inputs:
+ max_shards:
+ description: "Maximum number of shards allowed"
+ required: true
+ paths:
+ description: "Component paths to test"
+ required: false
+ tags:
+ description: "Tags to pass as argument for nf-test --tag parameter"
+ required: false
+outputs:
+ shard:
+ description: "Array of shard numbers"
+ value: ${{ steps.shards.outputs.shard }}
+ total_shards:
+ description: "Total number of shards"
+ value: ${{ steps.shards.outputs.total_shards }}
+runs:
+ using: "composite"
+ steps:
+ - name: Install nf-test
+ uses: nf-core/setup-nf-test@v1
+ with:
+ version: ${{ env.NFT_VER }}
+ - name: Get number of shards
+ id: shards
+ shell: bash
+ run: |
+ # Run nf-test with dynamic parameter
+ nftest_output=$(nf-test test \
+ --profile +docker \
+ $(if [ -n "${{ inputs.tags }}" ]; then echo "--tag ${{ inputs.tags }}"; fi) \
+ --dry-run \
+ --ci \
+ --changed-since HEAD^) || {
+ echo "nf-test command failed with exit code $?"
+ echo "Full output: $nftest_output"
+ exit 1
+ }
+ echo "nf-test dry-run output: $nftest_output"
+
+ # Default values for shard and total_shards
+ shard="[]"
+ total_shards=0
+
+ # Check if there are related tests
+ if echo "$nftest_output" | grep -q 'No tests to execute'; then
+ echo "No related tests found."
+ else
+ # Extract the number of related tests
+ number_of_shards=$(echo "$nftest_output" | sed -n 's|.*Executed \([0-9]*\) tests.*|\1|p')
+ if [[ -n "$number_of_shards" && "$number_of_shards" -gt 0 ]]; then
+ shards_to_run=$(( $number_of_shards < ${{ inputs.max_shards }} ? $number_of_shards : ${{ inputs.max_shards }} ))
+ shard=$(seq 1 "$shards_to_run" | jq -R . | jq -c -s .)
+ total_shards="$shards_to_run"
+ else
+ echo "Unexpected output format. Falling back to default values."
+ fi
+ fi
+
+ # Write to GitHub Actions outputs
+ echo "shard=$shard" >> $GITHUB_OUTPUT
+ echo "total_shards=$total_shards" >> $GITHUB_OUTPUT
+
+ # Debugging output
+ echo "Final shard array: $shard"
+ echo "Total number of shards: $total_shards"
diff --git a/.github/actions/nf-test/action.yml b/.github/actions/nf-test/action.yml
new file mode 100644
index 00000000..bf44d961
--- /dev/null
+++ b/.github/actions/nf-test/action.yml
@@ -0,0 +1,109 @@
+name: "nf-test Action"
+description: "Runs nf-test with common setup steps"
+inputs:
+ profile:
+ description: "Profile to use"
+ required: true
+ shard:
+ description: "Shard number for this CI job"
+ required: true
+ total_shards:
+ description: "Total number of test shards(NOT the total number of matrix jobs)"
+ required: true
+ paths:
+ description: "Test paths"
+ required: true
+ tags:
+ description: "Tags to pass as argument for nf-test --tag parameter"
+ required: false
+runs:
+ using: "composite"
+ steps:
+ - name: Setup Nextflow
+ uses: nf-core/setup-nextflow@v2
+ with:
+ version: "${{ env.NXF_VERSION }}"
+
+ - name: Set up Python
+ uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5
+ with:
+ python-version: "3.13"
+
+ - 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')
+ uses: eWaterCycle/setup-apptainer@main
+
+ - name: Set up Singularity
+ if: contains(inputs.profile, 'singularity')
+ shell: bash
+ run: |
+ mkdir -p $NXF_SINGULARITY_CACHEDIR
+ mkdir -p $NXF_SINGULARITY_LIBRARYDIR
+
+ - name: Conda setup
+ if: contains(inputs.profile, 'conda')
+ uses: conda-incubator/setup-miniconda@505e6394dae86d6a5c7fbb6e3fb8938e3e863830 # v3
+ with:
+ auto-update-conda: true
+ conda-solver: libmamba
+ conda-remove-defaults: true
+
+ - name: Run nf-test
+ shell: bash
+ env:
+ NFT_WORKDIR: ${{ env.NFT_WORKDIR }}
+ run: |
+ nf-test test \
+ --profile=+${{ inputs.profile }} \
+ $(if [ -n "${{ inputs.tags }}" ]; then echo "--tag ${{ inputs.tags }}"; fi) \
+ --ci \
+ --changed-since HEAD^ \
+ --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
+
+ - name: Generate test summary
+ if: always()
+ shell: bash
+ run: |
+ # Add header if it doesn't exist (using a token file to track this)
+ if [ ! -f ".summary_header" ]; then
+ echo "# 🚀 nf-test results" >> $GITHUB_STEP_SUMMARY
+ echo "" >> $GITHUB_STEP_SUMMARY
+ echo "| Status | Test Name | Profile | Shard |" >> $GITHUB_STEP_SUMMARY
+ echo "|:------:|-----------|---------|-------|" >> $GITHUB_STEP_SUMMARY
+ touch .summary_header
+ fi
+
+ if [ -f test.tap ]; then
+ while IFS= read -r line; do
+ if [[ $line =~ ^ok ]]; then
+ test_name="${line#ok }"
+ # Remove the test number from the beginning
+ test_name="${test_name#* }"
+ echo "| ✅ | ${test_name} | ${{ inputs.profile }} | ${{ inputs.shard }}/${{ inputs.total_shards }} |" >> $GITHUB_STEP_SUMMARY
+ elif [[ $line =~ ^not\ ok ]]; then
+ test_name="${line#not ok }"
+ # Remove the test number from the beginning
+ test_name="${test_name#* }"
+ echo "| ❌ | ${test_name} | ${{ inputs.profile }} | ${{ inputs.shard }}/${{ inputs.total_shards }} |" >> $GITHUB_STEP_SUMMARY
+ fi
+ done < test.tap
+ else
+ echo "| ⚠️ | No test results found | ${{ inputs.profile }} | ${{ inputs.shard }}/${{ inputs.total_shards }} |" >> $GITHUB_STEP_SUMMARY
+ fi
+
+ - name: Clean up
+ if: always()
+ shell: bash
+ run: |
+ sudo rm -rf /home/ubuntu/tests/
diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml
index 239b9ac4..212e0138 100644
--- a/.github/workflows/awsfulltest.yml
+++ b/.github/workflows/awsfulltest.yml
@@ -14,7 +14,7 @@ jobs:
run-platform:
name: Run AWS full tests
# run only if the PR is approved by at least 2 reviewers and against the master/main branch or manually triggered
- if: github.repository == 'nf-core/multiplesequencealign' && github.event.review.state == 'approved' && (github.event.pull_request.base.ref == 'master' || github.event.pull_request.base.ref == 'main') || github.event_name == 'workflow_dispatch'
+ if: github.repository == 'nf-core/multiplesequencealign' && github.event.review.state == 'approved' && (github.event.pull_request.base.ref == 'master' || github.event.pull_request.base.ref == 'main') || github.event_name == 'workflow_dispatch' || github.event_name == 'release'
runs-on: ubuntu-latest
steps:
- name: Set revision variable
@@ -37,7 +37,7 @@ jobs:
}
profiles: test_full
- - uses: actions/upload-artifact@v4
+ - uses: actions/upload-artifact@ea165f8d65b6e75b540449e92b4886f43607fa02 # v4
with:
name: Seqera Platform debug log file
path: |
diff --git a/.github/workflows/awstest.yml b/.github/workflows/awstest.yml
index f1cf60a5..8727692d 100644
--- a/.github/workflows/awstest.yml
+++ b/.github/workflows/awstest.yml
@@ -25,7 +25,7 @@ jobs:
}
profiles: test
- - uses: actions/upload-artifact@v4
+ - uses: actions/upload-artifact@ea165f8d65b6e75b540449e92b4886f43607fa02 # v4
with:
name: Seqera Platform debug log file
path: |
diff --git a/.github/workflows/clean-up.yml b/.github/workflows/clean-up.yml
index 0b6b1f27..ac030fd5 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@5bef64f19d7facfb25b37b414482c7164d639639 # v9
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 1f3a1b64..9d5ce8ca 100644
--- a/.github/workflows/download_pipeline.yml
+++ b/.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@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
+ - uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5
with:
- python-version: "3.12"
+ python-version: "3.13"
architecture: "x64"
- name: Setup Apptainer
@@ -112,6 +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 }}
@@ -124,3 +125,10 @@ jobs:
else
echo "The pipeline can be downloaded successfully!"
fi
+
+ - name: Upload Nextflow logfile for debugging purposes
+ uses: actions/upload-artifact@ea165f8d65b6e75b540449e92b4886f43607fa02 # v4
+ 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 96%
rename from .github/workflows/fix-linting.yml
rename to .github/workflows/fix_linting.yml
index 3838bc30..7bc6c02e 100644
--- a/.github/workflows/fix-linting.yml
+++ b/.github/workflows/fix_linting.yml
@@ -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@a26af69be951a213d495a4c3e4e4022e16d87065 # v5
with:
- python-version: "3.12"
+ python-version: "3.13"
- name: Install pre-commit
run: pip install pre-commit
diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml
index dbd52d5a..8b0f88c3 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]
@@ -16,10 +13,10 @@ jobs:
steps:
- uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
- - name: Set up Python 3.12
- uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
+ - name: Set up Python 3.13
+ uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5
with:
- python-version: "3.12"
+ python-version: "3.13"
- name: Install pre-commit
run: pip install pre-commit
@@ -36,13 +33,13 @@ jobs:
- name: Install Nextflow
uses: nf-core/setup-nextflow@v2
- - uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
+ - uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5
with:
- python-version: "3.12"
+ python-version: "3.13"
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: ${{ always() }}
- uses: actions/upload-artifact@b4b15b8c7c6ac21ea08fcf65892d2ee8f75cf882 # v4
+ uses: actions/upload-artifact@ea165f8d65b6e75b540449e92b4886f43607fa02 # v4
with:
name: linting-logs
path: |
diff --git a/.github/workflows/linting_comment.yml b/.github/workflows/linting_comment.yml
index 95b6b6af..d43797d9 100644
--- a/.github/workflows/linting_comment.yml
+++ b/.github/workflows/linting_comment.yml
@@ -11,7 +11,7 @@ jobs:
runs-on: ubuntu-latest
steps:
- name: Download lint results
- uses: dawidd6/action-download-artifact@20319c5641d495c8a52e688b7dc5fada6c3a9fbc # v8
+ uses: dawidd6/action-download-artifact@ac66b43f0e6a346234dd65d4d0c8fbb31cb316e5 # v11
with:
workflow: linting.yml
workflow_conclusion: completed
@@ -21,7 +21,7 @@ jobs:
run: echo "pr_number=$(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@52423e01640425a022ef5fd42c6fb5f633a02728 # 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
new file mode 100644
index 00000000..e7b58449
--- /dev/null
+++ b/.github/workflows/nf-test.yml
@@ -0,0 +1,143 @@
+name: Run nf-test
+on:
+ pull_request:
+ paths-ignore:
+ - "docs/**"
+ - "**/meta.yml"
+ - "**/*.md"
+ - "**/*.png"
+ - "**/*.svg"
+ release:
+ types: [published]
+ workflow_dispatch:
+
+# Cancel if a newer run is started
+concurrency:
+ group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
+ cancel-in-progress: true
+
+env:
+ GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+ NFT_VER: "0.9.2"
+ NFT_WORKDIR: "~"
+ NXF_ANSI_LOG: false
+ NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity
+ NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity
+
+jobs:
+ nf-test-changes:
+ name: nf-test-changes
+ runs-on: # use self-hosted runners
+ - runs-on=${{ github.run_id }}-nf-test-changes
+ - runner=4cpu-linux-x64
+ outputs:
+ shard: ${{ steps.set-shards.outputs.shard }}
+ total_shards: ${{ steps.set-shards.outputs.total_shards }}
+ steps:
+ - name: Clean Workspace # Purge the workspace in case it's running on a self-hosted runner
+ run: |
+ ls -la ./
+ rm -rf ./* || true
+ rm -rf ./.??* || true
+ ls -la ./
+ - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
+ with:
+ fetch-depth: 0
+
+ - name: get number of shards
+ id: set-shards
+ uses: ./.github/actions/get-shards
+ env:
+ NFT_VER: ${{ env.NFT_VER }}
+ with:
+ max_shards: 7
+
+ - name: debug
+ run: |
+ echo ${{ steps.set-shards.outputs.shard }}
+ echo ${{ steps.set-shards.outputs.total_shards }}
+
+ nf-test:
+ name: "${{ matrix.profile }} | ${{ matrix.NXF_VER }} | ${{ matrix.shard }}/${{ needs.nf-test-changes.outputs.total_shards }}"
+ needs: [nf-test-changes]
+ if: ${{ needs.nf-test-changes.outputs.total_shards != '0' }}
+ runs-on: # use self-hosted runners
+ - runs-on=${{ github.run_id }}-nf-test
+ - runner=4cpu-linux-x64
+ strategy:
+ fail-fast: false
+ matrix:
+ shard: ${{ fromJson(needs.nf-test-changes.outputs.shard) }}
+ profile: [conda, docker, singularity]
+ isMain:
+ - ${{ github.base_ref == 'master' || github.base_ref == 'main' }}
+ # Exclude conda and singularity on dev
+ exclude:
+ - isMain: false
+ profile: "conda"
+ - isMain: false
+ profile: "singularity"
+ NXF_VER:
+ - "24.10.5"
+ - "latest-everything"
+ env:
+ NXF_ANSI_LOG: false
+ TOTAL_SHARDS: ${{ needs.nf-test-changes.outputs.total_shards }}
+
+ steps:
+ - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
+ 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_WORKDIR: ${{ env.NFT_WORKDIR }}
+ with:
+ profile: ${{ matrix.profile }}
+ shard: ${{ matrix.shard }}
+ total_shards: ${{ env.TOTAL_SHARDS }}
+
+ - 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 [[ "${{ matrix.NXF_VER }}" != "latest-everything" ]]; then
+ exit 1
+ fi
+ fi
+
+ confirm-pass:
+ needs: [nf-test]
+ if: always()
+ runs-on: # use self-hosted runners
+ - runs-on=${{ github.run_id }}-confirm-pass
+ - runner=2cpu-linux-x64
+ steps:
+ - name: One or more tests failed (excluding latest-everything)
+ if: ${{ contains(needs.*.result, 'failure') }}
+ run: exit 1
+
+ - name: One or more tests cancelled
+ if: ${{ contains(needs.*.result, 'cancelled') }}
+ run: exit 1
+
+ - name: All tests ok
+ if: ${{ contains(needs.*.result, 'success') }}
+ run: exit 0
+
+ - name: debug-print
+ if: always()
+ run: |
+ echo "::group::DEBUG: `needs` Contents"
+ echo "DEBUG: toJSON(needs) = ${{ toJSON(needs) }}"
+ echo "DEBUG: toJSON(needs.*.result) = ${{ toJSON(needs.*.result) }}"
+ echo "::endgroup::"
diff --git a/.github/workflows/release-announcements.yml b/.github/workflows/release-announcements.yml
index 76a9e67e..0f732495 100644
--- a/.github/workflows/release-announcements.yml
+++ b/.github/workflows/release-announcements.yml
@@ -30,7 +30,7 @@ jobs:
bsky-post:
runs-on: ubuntu-latest
steps:
- - uses: zentered/bluesky-post-action@80dbe0a7697de18c15ad22f4619919ceb5ccf597 # v0.1.0
+ - 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 }}!
diff --git a/.github/workflows/template_version_comment.yml b/.github/workflows/template-version-comment.yml
similarity index 95%
rename from .github/workflows/template_version_comment.yml
rename to .github/workflows/template-version-comment.yml
index 537529bc..beb5c77f 100644
--- a/.github/workflows/template_version_comment.yml
+++ b/.github/workflows/template-version-comment.yml
@@ -14,7 +14,7 @@ jobs:
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: ${{ github.workspace }}/.nf-core.yml
diff --git a/.nf-core.yml b/.nf-core.yml
index ca118298..fd3b556b 100644
--- a/.nf-core.yml
+++ b/.nf-core.yml
@@ -1,12 +1,11 @@
lint:
- actions_ci: false # TODO: remove this with nf-core template version 3.3.0
files_exist:
- conf/igenomes.config
- conf/igenomes_ignored.config
files_unchanged:
- .github/CONTRIBUTING.md
multiqc_config: false
-nf_core_version: 3.2.1
+nf_core_version: 3.3.2
repository_type: pipeline
template:
author: Luisa Santus, Jose Espinosa-Carrasco
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 1dec8650..bb41beec 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -4,10 +4,24 @@ repos:
hooks:
- id: prettier
additional_dependencies:
- - prettier@3.2.5
-
- - repo: https://github.com/editorconfig-checker/editorconfig-checker.python
- rev: "3.1.2"
+ - prettier@3.6.2
+ - repo: https://github.com/pre-commit/pre-commit-hooks
+ rev: v5.0.0
hooks:
- - id: editorconfig-checker
- alias: ec
+ - id: trailing-whitespace
+ args: [--markdown-linebreak-ext=md]
+ exclude: |
+ (?x)^(
+ .*ro-crate-metadata.json$|
+ 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/.prettierrc.yml b/.prettierrc.yml
index c81f9a76..07dbd8bb 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 8aa143f5..6d05b0c3 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -3,7 +3,7 @@
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).
-## 1.2.0
+## v1.2.0dev
### Enhancements & fixes
diff --git a/README.md b/README.md
index d0375a43..2da37d5d 100644
--- a/README.md
+++ b/README.md
@@ -5,17 +5,18 @@
-[](https://github.com/nf-core/multiplesequencealign/actions/workflows/ci.yml)
+[](https://github.com/nf-core/multiplesequencealign/actions/workflows/nf-test.yml)
[](https://github.com/nf-core/multiplesequencealign/actions/workflows/linting.yml)[](https://nf-co.re/multiplesequencealign/results)[](https://doi.org/10.5281/zenodo.13889386)
[](https://www.nf-test.com)
-[](https://www.nextflow.io/)
+[](https://www.nextflow.io/)
+[](https://github.com/nf-core/tools/releases/tag/3.3.2)
[](https://docs.conda.io/en/latest/)
[](https://www.docker.com/)
[](https://sylabs.io/docs/)
[](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/multiplesequencealign)
-[](https://nfcore.slack.com/channels/multiplesequencealign)[](https://twitter.com/nf_core)[](https://mstdn.science/@nf_core)[](https://www.youtube.com/c/nf-core)
+[](https://nfcore.slack.com/channels/multiplesequencealign)[](https://bsky.app/profile/nf-co.re)[](https://mstdn.science/@nf_core)[](https://www.youtube.com/c/nf-core)
## Introduction
diff --git a/conf/base.config b/conf/base.config
index 749478db..53c37960 100644
--- a/conf/base.config
+++ b/conf/base.config
@@ -14,8 +14,8 @@ process {
memory = { 6.GB * task.attempt }
time = { 4.h * task.attempt }
- errorStrategy = { task.exitStatus in ((130..145) + 104) ? 'retry' : 'finish' }
- maxRetries = 3
+ errorStrategy = { task.exitStatus in ((130..145) + 104 + 175) ? 'retry' : 'finish' }
+ maxRetries = 1
maxErrors = '-1'
// Process-specific resource requirements
@@ -57,7 +57,10 @@ process {
errorStrategy = 'retry'
maxRetries = 2
}
-
+ withLabel: process_gpu {
+ ext.use_gpu = { workflow.profile.contains('gpu') }
+ accelerator = { workflow.profile.contains('gpu') ? 1 : null }
+ }
withName: "LEARNMSA_ALIGN"{
cpus = { 4 * task.attempt }
memory = { 20.GB * task.attempt }
diff --git a/docs/usage/adding_a_tool.md b/docs/usage/adding_a_tool.md
index 0d5dfb4c..759b1199 100644
--- a/docs/usage/adding_a_tool.md
+++ b/docs/usage/adding_a_tool.md
@@ -23,7 +23,6 @@ These steps will guide you to include a new MSA tool into the pipeline. Once don
- [ ] **1.** **Fork** this repository and create a **new branch** (e.g. add-famsa)
- [ ] **2. Include the module in the alignment subworkflow** (`subworkflows/local/align.nf`)
-
- [ ] Install the module. E.g. with the command `nf-core modules install famsa/align`.
- [ ] Include the module in `subworkflows/local/align.nf`, example [here](https://github.com/nf-core/multiplesequencealign/blob/4623d19f68b20f0ab16410eba496c329e4f31fa3/subworkflows/local/align.nf#L12).
- [ ] Add a branch to the correct channel, depending on your tool input. Example for sequence-based tools [here](https://github.com/nf-core/multiplesequencealign/blob/4623d19f68b20f0ab16410eba496c329e4f31fa3/subworkflows/local/align.nf#L83) and structure-based [here](https://github.com/nf-core/multiplesequencealign/blob/4623d19f68b20f0ab16410eba496c329e4f31fa3/subworkflows/local/align.nf#L101).
@@ -32,7 +31,6 @@ These steps will guide you to include a new MSA tool into the pipeline. Once don
- [ ] **3.** Add the aligner to the **aligner config** in [conf/modules.config](https://github.com/nf-core/multiplesequencealign/blob/dev/conf/modules.config). [Example](https://github.com/nf-core/multiplesequencealign/blob/4623d19f68b20f0ab16410eba496c329e4f31fa3/conf/modules.config#L125-L143).
- [ ] **4. Update Docs**
-
- [ ] Update docs/usage.md
- [ ] Update CITATIONS.md
- [ ] Update CHANGELOG.md
@@ -56,7 +54,6 @@ Adding a new evaluation mainly requires changes in the [evaluate.nf](https://git
- [ ] **1.** **Fork** this repository and create a **new branch** (e.g. add-tcoffee-alncompare)
- [ ] **2. Include the module in the evaluate subworkflow** (`subworkflows/local/evaluate.nf`)
-
- [ ] Add a `calc_yourscore` parameter to the pipeline in `nextflow.config` and document it in `nextflow_schema.json`. The parameter can then be passed by the user to decide whether to run your evaluation workflow. [Example](https://github.com/nf-core/multiplesequencealign/blob/4623d19f68b20f0ab16410eba496c329e4f31fa3/nextflow.config#L32).
- [ ] Add a codeblock to `subworkflows/local/evaluate` that calls the newly added evaluation module if the appropriate parameter is passed to the pipeline. [Example](https://github.com/nf-core/multiplesequencealign/blob/4623d19f68b20f0ab16410eba496c329e4f31fa3/subworkflows/local/evaluate.nf#L59-L77).
- [ ] To ensure the called module produces an output file with the correct name for merging evaluation outputs, add a config option in `conf/modules.config`. [Example](https://github.com/nf-core/multiplesequencealign/blob/4623d19f68b20f0ab16410eba496c329e4f31fa3/conf/modules.config#L189-L192).
diff --git a/modules.json b/modules.json
index 78514f49..77162457 100644
--- a/modules.json
+++ b/modules.json
@@ -43,7 +43,7 @@
},
"fastqc": {
"branch": "master",
- "git_sha": "81880787133db07d9b4c1febd152c090eb8325dc",
+ "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
"installed_by": ["modules"]
},
"foldmason/createdb": {
@@ -95,7 +95,7 @@
},
"multiqc": {
"branch": "master",
- "git_sha": "81880787133db07d9b4c1febd152c090eb8325dc",
+ "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
"installed_by": ["modules"]
},
"muscle5/super5": {
diff --git a/modules/nf-core/fastqc/environment.yml b/modules/nf-core/fastqc/environment.yml
new file mode 100644
index 00000000..f9f54ee9
--- /dev/null
+++ b/modules/nf-core/fastqc/environment.yml
@@ -0,0 +1,7 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+channels:
+ - conda-forge
+ - bioconda
+dependencies:
+ - bioconda::fastqc=0.12.1
diff --git a/modules/nf-core/fastqc/main.nf b/modules/nf-core/fastqc/main.nf
index 033f4154..23e16634 100644
--- a/modules/nf-core/fastqc/main.nf
+++ b/modules/nf-core/fastqc/main.nf
@@ -29,7 +29,7 @@ process FASTQC {
// The total amount of allocated RAM by FastQC is equal to the number of threads defined (--threads) time the amount of RAM defined (--memory)
// https://github.com/s-andrews/FastQC/blob/1faeea0412093224d7f6a07f777fad60a5650795/fastqc#L211-L222
// Dividing the task.memory by task.cpu allows to stick to requested amount of RAM in the label
- def memory_in_mb = task.memory ? task.memory.toUnit('MB').toFloat() / task.cpus : null
+ def memory_in_mb = task.memory ? task.memory.toUnit('MB') / task.cpus : null
// FastQC memory value allowed range (100 - 10000)
def fastqc_memory = memory_in_mb > 10000 ? 10000 : (memory_in_mb < 100 ? 100 : memory_in_mb)
diff --git a/modules/nf-core/fastqc/meta.yml b/modules/nf-core/fastqc/meta.yml
index 2b2e62b8..c8d9d025 100644
--- a/modules/nf-core/fastqc/meta.yml
+++ b/modules/nf-core/fastqc/meta.yml
@@ -29,9 +29,10 @@ input:
description: |
List of input FastQ files of size 1 and 2 for single-end and paired-end data,
respectively.
+ ontologies: []
output:
- - html:
- - meta:
+ html:
+ - - meta:
type: map
description: |
Groovy Map containing sample information
@@ -40,8 +41,9 @@ output:
type: file
description: FastQC report
pattern: "*_{fastqc.html}"
- - zip:
- - meta:
+ ontologies: []
+ zip:
+ - - meta:
type: map
description: |
Groovy Map containing sample information
@@ -50,11 +52,14 @@ output:
type: file
description: FastQC report archive
pattern: "*_{fastqc.zip}"
- - versions:
- - versions.yml:
- type: file
- description: File containing software versions
- pattern: "versions.yml"
+ ontologies: []
+ versions:
+ - versions.yml:
+ type: file
+ description: File containing software versions
+ pattern: "versions.yml"
+ ontologies:
+ - edam: http://edamontology.org/format_3750 # YAML
authors:
- "@drpatelh"
- "@grst"
diff --git a/modules/nf-core/multiqc/environment.yml b/modules/nf-core/multiqc/environment.yml
index c3b3413f..812fc4c5 100644
--- a/modules/nf-core/multiqc/environment.yml
+++ b/modules/nf-core/multiqc/environment.yml
@@ -4,4 +4,4 @@ channels:
- conda-forge
- bioconda
dependencies:
- - bioconda::multiqc=1.27
+ - bioconda::multiqc=1.29
diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf
index 58d9313c..0ac3c369 100644
--- a/modules/nf-core/multiqc/main.nf
+++ b/modules/nf-core/multiqc/main.nf
@@ -3,8 +3,8 @@ 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://depot.galaxyproject.org/singularity/multiqc:1.29--pyhdfd78af_0' :
+ 'biocontainers/multiqc:1.29--pyhdfd78af_0' }"
input:
path multiqc_files, stageAs: "?/*"
diff --git a/modules/nf-core/multiqc/meta.yml b/modules/nf-core/multiqc/meta.yml
index b16c1879..ce30eb73 100644
--- a/modules/nf-core/multiqc/meta.yml
+++ b/modules/nf-core/multiqc/meta.yml
@@ -15,57 +15,71 @@ 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:
+ - 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:
+ - "*multiqc_report.html":
type: file
- description: Optional logo file for MultiQC
- pattern: "*.{png}"
- - - replace_names:
+ description: MultiQC report file
+ pattern: "multiqc_report.html"
+ ontologies: []
+ data:
+ - "*_data":
+ type: directory
+ description: MultiQC data dir
+ pattern: "multiqc_data"
+ plots:
+ - "*_plots":
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: Plots created by MultiQC
+ pattern: "*_data"
+ ontologies: []
+ versions:
+ - versions.yml:
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: File containing software versions
+ pattern: "versions.yml"
+ ontologies:
+ - edam: http://edamontology.org/format_3750 # YAML
authors:
- "@abhi18av"
- "@bunop"
diff --git a/modules/nf-core/multiqc/tests/main.nf.test.snap b/modules/nf-core/multiqc/tests/main.nf.test.snap
index 7b7c1322..88e90571 100644
--- a/modules/nf-core/multiqc/tests/main.nf.test.snap
+++ b/modules/nf-core/multiqc/tests/main.nf.test.snap
@@ -2,14 +2,14 @@
"multiqc_versions_single": {
"content": [
[
- "versions.yml:md5,8f3b8c1cec5388cf2708be948c9fa42f"
+ "versions.yml:md5,c1fe644a37468f6dae548d98bc72c2c1"
]
],
"meta": {
"nf-test": "0.9.2",
- "nextflow": "24.10.4"
+ "nextflow": "25.04.2"
},
- "timestamp": "2025-01-27T09:29:57.631982377"
+ "timestamp": "2025-05-22T11:50:41.182332996"
},
"multiqc_stub": {
"content": [
@@ -17,25 +17,25 @@
"multiqc_report.html",
"multiqc_data",
"multiqc_plots",
- "versions.yml:md5,8f3b8c1cec5388cf2708be948c9fa42f"
+ "versions.yml:md5,c1fe644a37468f6dae548d98bc72c2c1"
]
],
"meta": {
"nf-test": "0.9.2",
- "nextflow": "24.10.4"
+ "nextflow": "25.04.2"
},
- "timestamp": "2025-01-27T09:30:34.743726958"
+ "timestamp": "2025-05-22T11:51:22.448739369"
},
"multiqc_versions_config": {
"content": [
[
- "versions.yml:md5,8f3b8c1cec5388cf2708be948c9fa42f"
+ "versions.yml:md5,c1fe644a37468f6dae548d98bc72c2c1"
]
],
"meta": {
"nf-test": "0.9.2",
- "nextflow": "24.10.4"
+ "nextflow": "25.04.2"
},
- "timestamp": "2025-01-27T09:30:21.44383553"
+ "timestamp": "2025-05-22T11:51:06.198928424"
}
}
\ No newline at end of file
diff --git a/nextflow.config b/nextflow.config
index 03114464..63a78e99 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -203,6 +203,11 @@ profiles {
]
}
}
+ gpu {
+ docker.runOptions = '-u $(id -u):$(id -g) --gpus all'
+ apptainer.runOptions = '--nv'
+ singularity.runOptions = '--nv'
+ }
test { includeConfig 'conf/test.config' }
test_full { includeConfig 'conf/test_full.config' }
test_tiny { includeConfig 'conf/test_tiny.config' }
@@ -212,8 +217,12 @@ profiles {
easy_deploy { includeConfig 'conf/easy_deploy.config' }
}
-// Load nf-core custom profiles from different Institutions
-includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/nfcore_custom.config" : "/dev/null"
+// Load nf-core custom profiles from different institutions
+
+// If params.custom_config_base is set AND either the NXF_OFFLINE environment variable is not set or params.custom_config_base is a local path, the nfcore_custom.config file from the specified base path is included.
+// Load nf-core/multiplesequencealign custom profiles from different institutions.
+includeConfig params.custom_config_base && (!System.getenv('NXF_OFFLINE') || !params.custom_config_base.startsWith('http')) ? "${params.custom_config_base}/nfcore_custom.config" : "/dev/null"
+
// Load nf-core/multiplesequencealign custom profiles from different institutions.
includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/pipeline/multiplesequencealign.config" : "/dev/null"
@@ -332,7 +341,7 @@ manifest {
// 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@2.4.2' // Validation of pipeline parameters and creation of an input channel from a sample sheet
id 'nf-co2footprint@1.0.0-beta'
id 'nf-prov@1.2.2' // Provenance reports for pipeline runs
}
diff --git a/nf-test.config b/nf-test.config
index a2f9e1b2..3a1fff59 100644
--- a/nf-test.config
+++ b/nf-test.config
@@ -1,8 +1,24 @@
config {
-
+ // location for all nf-test tests
testsDir "."
+
+ // nf-test directory including temporary files for each test
workDir System.getenv("NFT_WORKDIR") ?: ".nf-test"
+
+ // location of an optional nextflow.config file specific for executing tests
configFile "tests/nextflow.config"
+
+ // ignore tests coming from the nf-core/modules repo
+ ignore 'modules/nf-core/**/tests/*', 'subworkflows/nf-core/**/tests/*'
+
+ // run all test with defined profile(s) from the main nextflow.config
profile "test"
+ // list of filenames or patterns that should be trigger a full test run
+ triggers 'nextflow.config', 'nf-test.config', 'conf/test.config', 'tests/nextflow.config', 'tests/.nftignore'
+
+ // load the necessary plugins
+ plugins {
+ load "nft-utils@0.0.3"
+ }
}
diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json
index a9835ae5..cde17c9f 100644
--- a/ro-crate-metadata.json
+++ b/ro-crate-metadata.json
@@ -22,8 +22,8 @@
"@id": "./",
"@type": "Dataset",
"creativeWorkStatus": "InProgress",
- "datePublished": "2025-05-27T19:35:14+00:00",
- "description": "
\n \n \n \n \n
\n\n[](https://github.com/nf-core/multiplesequencealign/actions/workflows/ci.yml)\n[](https://github.com/nf-core/multiplesequencealign/actions/workflows/linting.yml)[](https://nf-co.re/multiplesequencealign/results)[](https://doi.org/10.5281/zenodo.13889386)\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://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/multiplesequencealign)\n\n[](https://nfcore.slack.com/channels/multiplesequencealign)[](https://twitter.com/nf_core)[](https://mstdn.science/@nf_core)[](https://www.youtube.com/c/nf-core)\n\n## Introduction\n\nUse **nf-core/multiplesequencealign** to:\n\n1. **Deploy** one (or many) of the most popular Multiple Sequence Alignment (MSA) tools.\n2. **Benchmark** MSA tools (and their inputs) using various metrics.\n\nMain steps:\n\n \n Inputs summary (Optional)\n
Computation of summary statistics on the input files (e.g., average sequence similarity across the input sequences, their length, pLDDT extraction if available).
\n \n\n \n Guide Tree (Optional)\n
Renders a guide tree with a chosen tool (list available in usage). Some aligners use guide trees to define the order in which the sequences are aligned.
\n \n\n \n Align (Required)\n
Aligns the sequences with a chosen tool (list available in usage).
\n \n\n \n Evaluate (Optional)\n
Evaluates the generated alignments with different metrics: Sum Of Pairs (SoP), Total Column score (TC), iRMSD, Total Consistency Score (TCS), etc.
\n \n\n \n Report(Optional)\n
Reports the collected information of the runs in a Shiny app and a summary table in MultiQC. Optionally, it can also render the Foldmason MSA visualization in HTML format.
\n \n\n \n\nMore introductory material: [bytesize talk](https://youtu.be/iRY-Y1p5gtc), [nextflow summit talk](https://www.youtube.com/watch?v=suNulysHIN0), [poster](https://github.com/nf-core/multiplesequencealign/blob/dev/docs/images/poster-nf-msa.pdf).\n\n![Alt text](docs/images/nf-core-msa_metro_map.png?raw=true \"nf-core-msa metro map\")\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\n### Quick start - test run\n\nTo get a feeling of what the pipeline does, run:\n\n(You don't need to download or provide any file, try it!)\n\n```\nnextflow run nf-core/multiplesequencealign \\\n -profile test_tiny,docker \\\n --outdir results\n```\n\nand if you want to see how a more complete run looks like, you can try:\n\n```\nnextflow run nf-core/multiplesequencealign \\\n -profile test,docker \\\n --outdir results\n```\n\n## How to set up an easy run:\n\n> [!NOTE]\n> We have a lot more of use cases examples under [FAQs](\"https://nf-co.re/multiplesequencealign/usage/FAQs)\n\n### Input data\n\nYou can provide either (or both) a **fasta** file or a set of **protein structures**.\n\nAlternatively, you can provide a [samplesheet](https://nf-co.re/multiplesequencealign/usage/#samplesheet-input) and a [toolsheet](https://nf-co.re/multiplesequencealign/usage/#toolsheet-input).\n\nSee below how to provide them.\n\n> Find some example input data [here](https://github.com/nf-core/test-datasets/tree/multiplesequencealign)\n\n### CASE 1: One input dataset, one tool.\n\nIf you only have one dataset and want to align it using one specific MSA tool (e.g. FAMSA or FOLDMASON), you can run the pipeline with one single command.\n\nIs your input a fasta file ([example](https://github.com/nf-core/test-datasets/blob/multiplesequencealign/testdata/setoxin-ref.fa))? Then:\n\n```bash\nnextflow run nf-core/multiplesequencealign \\\n -profile easy_deploy,docker \\\n --seqs \\\n --aligner FAMSA \\\n --outdir outdir\n```\n\nIs your input a directory where your PDB files are stored ([example](https://github.com/nf-core/test-datasets/blob/multiplesequencealign/testdata/af2_structures/seatoxin-ref.tar.gz))? Then:\n\n```bash\nnextflow run nf-core/multiplesequencealign \\\n -profile easy_deploy,docker \\\n --pdbs_dir \\\n --aligner FOLDMASON \\\n --outdir outdir\n```\n\n\n FAQ: Which are the available tools I can use?\n Check the list here: available tools.\n\n\n\n FAQ: Can I use both --seqs and --pdbs_dir?\n Yes, go for it! This might be useful if you want a structural evaluation of a sequence-based aligner for instance.\n\n\n\n FAQ: Can I specify also which guidetree to use? \n Yes, use the --tree flag. More info: usage and parameters.\n\n\n\n FAQ: Can I specify the arguments of the tools (tree and aligner)? \n Yes, use the --args_tree and --args_aligner flags. More info: usage and parameters.\n\n\n### CASE 2: Multiple datasets, multiple tools.\n\n```bash\nnextflow run nf-core/multiplesequencealign \\\n -profile test,docker \\\n --input \\\n --tools \\\n --outdir outdir\n```\n\nYou need **2 input files**:\n\n- **samplesheet** (your datasets)\n- **toolsheet** (which tools you want to use).\n\n\n What is a samplesheet?\n The sample sheet defines the input datasets (sequences, structures, etc.) that the pipeline will process.\n\nA minimal version:\n\n```csv\nid,fasta\nseatoxin,seatoxin.fa\ntoxin,toxin.fa\n```\n\nA more complete one:\n\n```csv\nid,fasta,reference,optional_data\nseatoxin,seatoxin.fa,seatoxin-ref.fa,seatoxin_structures\ntoxin,toxin.fa,toxin-ref.fa,toxin_structures\n```\n\nEach row represents a set of sequences (in this case the seatoxin and toxin protein families) to be aligned and the associated (if available) reference alignments and dependency files (this can be anything from protein structure or any other information you would want to use in your favourite MSA tool).\n\nPlease check: usage.\n\n> [!NOTE]\n> The only required input is the id column and either fasta or optional_data.\n\n\n\n\n What is a toolsheet?\n The toolsheet specifies which combination of tools will be deployed and benchmarked in the pipeline.\n\nEach line defines a combination of guide tree and multiple sequence aligner to run with the respective arguments to be used.\n\nThe only required field is `aligner`. The fields `tree`, `args_tree` and `args_aligner` are optional and can be left empty.\n\nA minimal version:\n\n```csv\ntree,args_tree,aligner,args_aligner\n,,FAMSA,\n```\n\nThis will run the FAMSA aligner.\n\nA more complex one:\n\n```csv\ntree,args_tree,aligner,args_aligner\nFAMSA, -gt upgma -medoidtree, FAMSA,\n, ,TCOFFEE,\nFAMSA,,REGRESSIVE,\n```\n\nThis will run, in parallel:\n\n- the FAMSA guidetree with the arguments -gt upgma -medoidtree. This guidetree is then used as input for the FAMSA aligner.\n- the TCOFFEE aligner\n- the FAMSA guidetree with default arguments. This guidetree is then used as input for the REGRESSIVE aligner.\n\nPlease check: usage.\n\n> [!NOTE]\n> The only required input is `aligner`.\n\n\n\nFor more details on more advanced runs: [usage documentation](https://nf-co.re/multiplesequencealign/usage) and the [parameter documentation](https://nf-co.re/multiplesequencealign/parameters).\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**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files).\n\n## Pipeline resources\n\nWhich resources is the pipeline using? You can find the default resources used in [base.config](conf/base.config).\n\nIf you are using specific profiles, e.g. [test](conf/test.config), these will overwrite the defaults.\n\nIf you want to modify the needed resources, please refer [usage](https://nf-co.re/multiplesequencealign/docs/usage/#custom-configuration).\n\n## Pipeline output\n\nExample results: [results](https://nf-co.re/multiplesequencealign/results) tab on the nf-core website pipeline page.\nFor more details: [output documentation](https://nf-co.re/multiplesequencealign/output).\n\n## Extending the pipeline\n\nFor details on how to add your favourite guide tree, MSA or evaluation step in nf-core/multiplesequencealign please refer to the [extending documentation](https://nf-co.re/multiplesequencealign/usage/adding_a_tool).\n\n## Credits\n\nnf-core/multiplesequencealign was originally written by Luisa Santus ([@luisas](https://github.com/luisas)) and Jose Espinosa-Carrasco ([@JoseEspinosa](https://github.com/JoseEspinosa)) from The Comparative Bioinformatics Group at The Centre for Genomic Regulation, Spain.\n\nThe following people have significantly contributed to the development of the pipeline and its modules: Leon Rauschning ([@lrauschning](https://github.com/lrauschning)), Alessio Vignoli ([@alessiovignoli](https://github.com/alessiovignoli)), Igor Trujnara ([@itrujnara](https://github.com/itrujnara)) and Leila Mansouri ([@l-mansouri](https://github.com/l-mansouri)).\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#multiplesequencealign` channel](https://nfcore.slack.com/channels/multiplesequencealign) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\nIf you use nf-core/multiplesequencealign for your analysis, please cite it using the following doi: [10.5281/zenodo.13889386](https://doi.org/10.5281/zenodo.13889386)\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\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",
+ "datePublished": "2025-07-08T11:38:29+00:00",
+ "description": "
\n \n \n \n \n
\n\n[](https://github.com/nf-core/multiplesequencealign/actions/workflows/nf-test.yml)\n[](https://github.com/nf-core/multiplesequencealign/actions/workflows/linting.yml)[](https://nf-co.re/multiplesequencealign/results)[](https://doi.org/10.5281/zenodo.13889386)\n[](https://www.nf-test.com)\n\n[](https://www.nextflow.io/)\n[](https://github.com/nf-core/tools/releases/tag/3.3.2)\n[](https://docs.conda.io/en/latest/)\n[](https://www.docker.com/)\n[](https://sylabs.io/docs/)\n[](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/multiplesequencealign)\n\n[](https://nfcore.slack.com/channels/multiplesequencealign)[](https://bsky.app/profile/nf-co.re)[](https://mstdn.science/@nf_core)[](https://www.youtube.com/c/nf-core)\n\n## Introduction\n\nUse **nf-core/multiplesequencealign** to:\n\n1. **Deploy** one (or many) of the most popular Multiple Sequence Alignment (MSA) tools.\n2. **Benchmark** MSA tools (and their inputs) using various metrics.\n\nMain steps:\n\n \n Inputs summary (Optional)\n
Computation of summary statistics on the input files (e.g., average sequence similarity across the input sequences, their length, pLDDT extraction if available).
\n \n\n \n Guide Tree (Optional)\n
Renders a guide tree with a chosen tool (list available in usage). Some aligners use guide trees to define the order in which the sequences are aligned.
\n \n\n \n Align (Required)\n
Aligns the sequences with a chosen tool (list available in usage).
\n \n\n \n Evaluate (Optional)\n
Evaluates the generated alignments with different metrics: Sum Of Pairs (SoP), Total Column score (TC), iRMSD, Total Consistency Score (TCS), etc.
\n \n\n \n Report(Optional)\n
Reports the collected information of the runs in a Shiny app and a summary table in MultiQC. Optionally, it can also render the Foldmason MSA visualization in HTML format.
\n \n\n \n\nMore introductory material: [bytesize talk](https://youtu.be/iRY-Y1p5gtc), [nextflow summit talk](https://www.youtube.com/watch?v=suNulysHIN0), [poster](https://github.com/nf-core/multiplesequencealign/blob/dev/docs/images/poster-nf-msa.pdf).\n\n![Alt text](docs/images/nf-core-msa_metro_map.png?raw=true \"nf-core-msa metro map\")\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\n### Quick start - test run\n\nTo get a feeling of what the pipeline does, run:\n\n(You don't need to download or provide any file, try it!)\n\n```\nnextflow run nf-core/multiplesequencealign \\\n -profile test_tiny,docker \\\n --outdir results\n```\n\nand if you want to see how a more complete run looks like, you can try:\n\n```\nnextflow run nf-core/multiplesequencealign \\\n -profile test,docker \\\n --outdir results\n```\n\n## How to set up an easy run:\n\n> [!NOTE]\n> We have a lot more of use cases examples under [FAQs](\"https://nf-co.re/multiplesequencealign/usage/FAQs)\n\n### Input data\n\nYou can provide either (or both) a **fasta** file or a set of **protein structures**.\n\nAlternatively, you can provide a [samplesheet](https://nf-co.re/multiplesequencealign/usage/#samplesheet-input) and a [toolsheet](https://nf-co.re/multiplesequencealign/usage/#toolsheet-input).\n\nSee below how to provide them.\n\n> Find some example input data [here](https://github.com/nf-core/test-datasets/tree/multiplesequencealign)\n\n### CASE 1: One input dataset, one tool.\n\nIf you only have one dataset and want to align it using one specific MSA tool (e.g. FAMSA or FOLDMASON), you can run the pipeline with one single command.\n\nIs your input a fasta file ([example](https://github.com/nf-core/test-datasets/blob/multiplesequencealign/testdata/setoxin-ref.fa))? Then:\n\n```bash\nnextflow run nf-core/multiplesequencealign \\\n -profile easy_deploy,docker \\\n --seqs \\\n --aligner FAMSA \\\n --outdir outdir\n```\n\nIs your input a directory where your PDB files are stored ([example](https://github.com/nf-core/test-datasets/blob/multiplesequencealign/testdata/af2_structures/seatoxin-ref.tar.gz))? Then:\n\n```bash\nnextflow run nf-core/multiplesequencealign \\\n -profile easy_deploy,docker \\\n --pdbs_dir \\\n --aligner FOLDMASON \\\n --outdir outdir\n```\n\n\n FAQ: Which are the available tools I can use?\n Check the list here: available tools.\n\n\n\n FAQ: Can I use both --seqs and --pdbs_dir?\n Yes, go for it! This might be useful if you want a structural evaluation of a sequence-based aligner for instance.\n\n\n\n FAQ: Can I specify also which guidetree to use? \n Yes, use the --tree flag. More info: usage and parameters.\n\n\n\n FAQ: Can I specify the arguments of the tools (tree and aligner)? \n Yes, use the --args_tree and --args_aligner flags. More info: usage and parameters.\n\n\n### CASE 2: Multiple datasets, multiple tools.\n\n```bash\nnextflow run nf-core/multiplesequencealign \\\n -profile test,docker \\\n --input \\\n --tools \\\n --outdir outdir\n```\n\nYou need **2 input files**:\n\n- **samplesheet** (your datasets)\n- **toolsheet** (which tools you want to use).\n\n\n What is a samplesheet?\n The sample sheet defines the input datasets (sequences, structures, etc.) that the pipeline will process.\n\nA minimal version:\n\n```csv\nid,fasta\nseatoxin,seatoxin.fa\ntoxin,toxin.fa\n```\n\nA more complete one:\n\n```csv\nid,fasta,reference,optional_data\nseatoxin,seatoxin.fa,seatoxin-ref.fa,seatoxin_structures\ntoxin,toxin.fa,toxin-ref.fa,toxin_structures\n```\n\nEach row represents a set of sequences (in this case the seatoxin and toxin protein families) to be aligned and the associated (if available) reference alignments and dependency files (this can be anything from protein structure or any other information you would want to use in your favourite MSA tool).\n\nPlease check: usage.\n\n> [!NOTE]\n> The only required input is the id column and either fasta or optional_data.\n\n\n\n\n What is a toolsheet?\n The toolsheet specifies which combination of tools will be deployed and benchmarked in the pipeline.\n\nEach line defines a combination of guide tree and multiple sequence aligner to run with the respective arguments to be used.\n\nThe only required field is `aligner`. The fields `tree`, `args_tree` and `args_aligner` are optional and can be left empty.\n\nA minimal version:\n\n```csv\ntree,args_tree,aligner,args_aligner\n,,FAMSA,\n```\n\nThis will run the FAMSA aligner.\n\nA more complex one:\n\n```csv\ntree,args_tree,aligner,args_aligner\nFAMSA, -gt upgma -medoidtree, FAMSA,\n, ,TCOFFEE,\nFAMSA,,REGRESSIVE,\n```\n\nThis will run, in parallel:\n\n- the FAMSA guidetree with the arguments -gt upgma -medoidtree. This guidetree is then used as input for the FAMSA aligner.\n- the TCOFFEE aligner\n- the FAMSA guidetree with default arguments. This guidetree is then used as input for the REGRESSIVE aligner.\n\nPlease check: usage.\n\n> [!NOTE]\n> The only required input is `aligner`.\n\n\n\nFor more details on more advanced runs: [usage documentation](https://nf-co.re/multiplesequencealign/usage) and the [parameter documentation](https://nf-co.re/multiplesequencealign/parameters).\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**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files).\n\n## Pipeline resources\n\nWhich resources is the pipeline using? You can find the default resources used in [base.config](conf/base.config).\n\nIf you are using specific profiles, e.g. [test](conf/test.config), these will overwrite the defaults.\n\nIf you want to modify the needed resources, please refer [usage](https://nf-co.re/multiplesequencealign/docs/usage/#custom-configuration).\n\n## Pipeline output\n\nExample results: [results](https://nf-co.re/multiplesequencealign/results) tab on the nf-core website pipeline page.\nFor more details: [output documentation](https://nf-co.re/multiplesequencealign/output).\n\n## Extending the pipeline\n\nFor details on how to add your favourite guide tree, MSA or evaluation step in nf-core/multiplesequencealign please refer to the [extending documentation](https://nf-co.re/multiplesequencealign/usage/adding_a_tool).\n\n## Credits\n\nnf-core/multiplesequencealign was originally written by Luisa Santus ([@luisas](https://github.com/luisas)) and Jose Espinosa-Carrasco ([@JoseEspinosa](https://github.com/JoseEspinosa)) from The Comparative Bioinformatics Group at The Centre for Genomic Regulation, Spain.\n\nThe following people have significantly contributed to the development of the pipeline and its modules: Leon Rauschning ([@lrauschning](https://github.com/lrauschning)), Alessio Vignoli ([@alessiovignoli](https://github.com/alessiovignoli)), Igor Trujnara ([@itrujnara](https://github.com/itrujnara)) and Leila Mansouri ([@l-mansouri](https://github.com/l-mansouri)).\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#multiplesequencealign` channel](https://nfcore.slack.com/channels/multiplesequencealign) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\nIf you use nf-core/multiplesequencealign for your analysis, please cite it using the following doi: [10.5281/zenodo.13889386](https://doi.org/10.5281/zenodo.13889386)\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\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"
@@ -108,7 +108,7 @@
},
"mentions": [
{
- "@id": "#fa597c9e-4d21-4766-bb51-3acefeb079de"
+ "@id": "#a8ef94cf-8c02-4748-b3b1-e05b80d475c3"
}
],
"name": "nf-core/multiplesequencealign"
@@ -141,7 +141,7 @@
}
],
"dateCreated": "",
- "dateModified": "2025-05-27T19:35:14Z",
+ "dateModified": "2025-07-08T11:38:29Z",
"dct:conformsTo": "https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE/",
"image": {
"@id": "docs/images/nf-core-msa_metro_map.png"
@@ -185,22 +185,14 @@
"url": {
"@id": "https://www.nextflow.io/"
},
- "version": "!>=25.04.2"
+ "version": "!>=24.10.5"
},
{
- "@id": "docs/images/nf-core-msa_metro_map.png",
- "@type": [
- "File",
- "ImageObject"
- ],
- "name": "Workflow diagram"
- },
- {
- "@id": "#fa597c9e-4d21-4766-bb51-3acefeb079de",
+ "@id": "#a8ef94cf-8c02-4748-b3b1-e05b80d475c3",
"@type": "TestSuite",
"instance": [
{
- "@id": "#3b0cfc14-21a1-4cff-a8ef-e13f3271c6d8"
+ "@id": "#76633d73-bd93-4c95-ac14-b9bf4004fc37"
}
],
"mainEntity": {
@@ -209,10 +201,10 @@
"name": "Test suite for nf-core/multiplesequencealign"
},
{
- "@id": "#3b0cfc14-21a1-4cff-a8ef-e13f3271c6d8",
+ "@id": "#76633d73-bd93-4c95-ac14-b9bf4004fc37",
"@type": "TestInstance",
"name": "GitHub Actions workflow for testing nf-core/multiplesequencealign",
- "resource": "repos/nf-core/multiplesequencealign/actions/workflows/ci.yml",
+ "resource": "repos/nf-core/multiplesequencealign/actions/workflows/nf-test.yml",
"runsOn": {
"@id": "https://w3id.org/ro/terms/test#GithubService"
},
diff --git a/subworkflows/local/utils_nfcore_multiplesequencealign_pipeline/main.nf b/subworkflows/local/utils_nfcore_multiplesequencealign_pipeline/main.nf
index 862409aa..9e43a490 100644
--- a/subworkflows/local/utils_nfcore_multiplesequencealign_pipeline/main.nf
+++ b/subworkflows/local/utils_nfcore_multiplesequencealign_pipeline/main.nf
@@ -306,8 +306,6 @@ def methodsDescriptionText(mqc_methods_yaml) {
return description_html.toString()
}
-
-
import groovy.transform.Field
/*
diff --git a/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config b/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config
index 0907ac58..09ef842a 100644
--- a/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config
+++ b/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config
@@ -1,5 +1,5 @@
plugins {
- id "nf-schema@2.1.0"
+ id "nf-schema@2.4.2"
}
validation {
diff --git a/tests/.nftignore b/tests/.nftignore
new file mode 100644
index 00000000..158c83c5
--- /dev/null
+++ b/tests/.nftignore
@@ -0,0 +1,11 @@
+.DS_Store
+multiqc/multiqc_data/fastqc_top_overrepresented_sequences_table.txt
+multiqc/multiqc_data/BETA-multiqc.parquet
+multiqc/multiqc_data/multiqc.log
+multiqc/multiqc_data/multiqc_data.json
+multiqc/multiqc_data/multiqc_sources.txt
+multiqc/multiqc_data/multiqc_software_versions.txt
+multiqc/multiqc_plots/{svg,pdf,png}/*.{svg,pdf,png}
+multiqc/multiqc_report.html
+fastqc/*_fastqc.{html,zip}
+pipeline_info/*.{html,json,txt,yml}
diff --git a/tests/default.nf.test b/tests/default.nf.test
new file mode 100644
index 00000000..ecda5b01
--- /dev/null
+++ b/tests/default.nf.test
@@ -0,0 +1,35 @@
+nextflow_pipeline {
+
+ name "Test pipeline"
+ script "../main.nf"
+ tag "pipeline"
+
+ test("-profile test") {
+
+ when {
+ params {
+ outdir = "$outputDir"
+ }
+ }
+
+ then {
+ // stable_name: All files + folders in ${params.outdir}/ with a stable name
+ def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}'])
+ // stable_path: All files in ${params.outdir}/ with stable content
+ def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore')
+ assertAll(
+ { assert workflow.success},
+ { assert snapshot(
+ // Number of successful tasks
+ workflow.trace.succeeded().size(),
+ // pipeline versions.yml file for multiqc from which Nextflow version is removed because we test pipelines on multiple Nextflow versions
+ removeNextflowVersion("$outputDir/pipeline_info/nf_core_multiplesequencealign_software_mqc_versions.yml"),
+ // All stable path name, with a relative path
+ stable_name,
+ // All files with stable contents
+ stable_path
+ ).match() }
+ )
+ }
+ }
+}
diff --git a/tests/nextflow.config b/tests/nextflow.config
index c02529cc..f05241cf 100644
--- a/tests/nextflow.config
+++ b/tests/nextflow.config
@@ -1,13 +1,17 @@
/*
========================================================================================
- Nextflow config file for running tests
+ Nextflow config file for running nf-test tests
========================================================================================
*/
params {
+ modules_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/'
+ pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/multiplesequencealign'
outdir = 'results'
}
+aws.client.anonymous = true // fixes S3 access issues on self-hosted runners
+
// Impose sensible resource limits for testing
process {
withName: '.*' {
![\"nf-core/multiplesequencealign\"](\"docs/images/nf-core-multiplesequencealign_logo_dark.png\"){kind=logo}
\n