From be762dabf37118442cef0c972678ddf0daa3a6e8 Mon Sep 17 00:00:00 2001 From: ljwharbers Date: Fri, 14 Aug 2026 15:33:38 +0200 Subject: [PATCH 1/6] Template update for nf-core/tools version 4.1.0 --- .devcontainer/setup.sh | 2 +- .github/ISSUE_TEMPLATE/bug_report.yml | 2 +- .github/ISSUE_TEMPLATE/config.yml | 6 +- .github/ISSUE_TEMPLATE/feature_request.yml | 2 +- .github/PULL_REQUEST_TEMPLATE.md | 8 +- .github/actions/nf-test/action.yml | 6 +- .github/workflows/branch.yml | 62 +- .github/workflows/clean-up.yml | 2 +- .github/workflows/download_pipeline.yml | 12 +- .github/workflows/fix_linting.yml | 10 +- .github/workflows/linting.yml | 34 +- .github/workflows/nf-test.yml | 61 +- .github/workflows/pr-comment.yml | 82 + .../workflows/template-version-comment.yml | 58 +- .hooks/block_pipeline_outdir.sh | 44 + .nf-core.yml | 24 +- .pre-commit-config.yaml | 19 +- CHANGELOG.md | 6 +- CITATIONS.md | 2 +- LICENSE | 2 +- README.md | 20 +- assets/email_template.html | 14 +- assets/email_template.txt | 8 +- assets/methods_description_template.yml | 8 +- assets/multiqc_config.yml | 6 +- assets/schema_input.json | 4 +- assets/sendmail_template.txt | 6 +- conf/base.config | 5 +- conf/containers_conda_lock_files_amd64.config | 2 +- conf/containers_conda_lock_files_arm64.config | 2 +- conf/containers_docker_amd64.config | 2 +- conf/containers_docker_arm64.config | 2 +- .../containers_singularity_https_amd64.config | 2 +- .../containers_singularity_https_arm64.config | 2 +- conf/containers_singularity_oras_amd64.config | 2 +- conf/containers_singularity_oras_arm64.config | 2 +- conf/igenomes.config | 856 +++++---- conf/modules.config | 3 +- conf/test.config | 2 +- conf/test_full.config | 2 +- docs/CONTRIBUTING.md | 22 +- docs/README.md | 4 +- docs/output.md | 4 +- docs/usage.md | 12 +- main.nf | 22 +- modules.json | 10 +- .../linux_amd64-bd-c17fb751507e9dfc_1.txt | 1526 +++++++++++++++++ .../linux_arm64-bd-5c84a5000a226ab5_1.txt | 1476 ++++++++++++++++ modules/nf-core/multiqc/environment.yml | 2 +- modules/nf-core/multiqc/main.nf | 4 +- modules/nf-core/multiqc/meta.yml | 28 +- .../nf-core/multiqc/tests/main.nf.test.snap | 10 +- nextflow.config | 16 +- nextflow_schema.json | 5 +- ro-crate-metadata.json | 45 +- .../main.nf | 5 +- .../nf-core/utils_nfschema_plugin/main.nf | 12 +- .../nf-core/utils_nfschema_plugin/meta.yml | 24 + .../utils_nfschema_plugin/tests/main.nf.test | 5 + .../tests/nextflow.config | 2 +- tests/default.nf.test | 2 +- tests/nextflow.config | 5 +- workflows/{lr_somatic.nf => lrsomatic.nf} | 8 +- 63 files changed, 3962 insertions(+), 681 deletions(-) create mode 100644 .github/workflows/pr-comment.yml create mode 100755 .hooks/block_pipeline_outdir.sh create mode 100644 modules/nf-core/multiqc/.conda-lock/linux_amd64-bd-c17fb751507e9dfc_1.txt create mode 100644 modules/nf-core/multiqc/.conda-lock/linux_arm64-bd-5c84a5000a226ab5_1.txt rename subworkflows/local/{utils_nfcore_lr_somatic_pipeline => utils_nfcore_lrsomatic_pipeline}/main.nf (99%) rename workflows/{lr_somatic.nf => lrsomatic.nf} (95%) diff --git a/.devcontainer/setup.sh b/.devcontainer/setup.sh index 70213d8a..1ab19682 100755 --- a/.devcontainer/setup.sh +++ b/.devcontainer/setup.sh @@ -10,4 +10,4 @@ export PS1='\[\e[3;36m\]\w ->\[\e[0m\\] ' nextflow self-update # Update welcome message -echo "Welcome to the IntGenomicsLab/lr_somatic devcontainer!" > /usr/local/etc/vscode-dev-containers/first-run-notice.txt +echo "Welcome to the IntGenomicsLab/lrsomatic devcontainer!" > /usr/local/etc/vscode-dev-containers/first-run-notice.txt diff --git a/.github/ISSUE_TEMPLATE/bug_report.yml b/.github/ISSUE_TEMPLATE/bug_report.yml index 1cd94f85..458770e1 100644 --- a/.github/ISSUE_TEMPLATE/bug_report.yml +++ b/.github/ISSUE_TEMPLATE/bug_report.yml @@ -39,4 +39,4 @@ body: * Executor _(eg. slurm, local, awsbatch)_ * Container engine: _(e.g. Docker, Singularity, Conda, Podman, Shifter, Charliecloud, or Apptainer)_ * OS _(eg. CentOS Linux, macOS, Linux Mint)_ - * Version of IntGenomicsLab/lr_somatic _(eg. 1.1, 1.5, 1.8.2)_ + * Version of IntGenomicsLab/lrsomatic _(eg. 1.1, 1.5, 1.8.2)_ diff --git a/.github/ISSUE_TEMPLATE/config.yml b/.github/ISSUE_TEMPLATE/config.yml index 04204ee5..7f210a1e 100644 --- a/.github/ISSUE_TEMPLATE/config.yml +++ b/.github/ISSUE_TEMPLATE/config.yml @@ -2,6 +2,6 @@ contact_links: - name: Join nf-core url: https://nf-co.re/join about: Please join the nf-core community here - - name: "Slack #lr_somatic channel" - url: https://nfcore.slack.com/channels/lr_somatic - about: Discussion about the IntGenomicsLab/lr_somatic pipeline + - name: "Slack #lrsomatic channel" + url: https://nfcore.slack.com/channels/lrsomatic + about: Discussion about the IntGenomicsLab/lrsomatic pipeline diff --git a/.github/ISSUE_TEMPLATE/feature_request.yml b/.github/ISSUE_TEMPLATE/feature_request.yml index 8a49b9b9..0e27f761 100644 --- a/.github/ISSUE_TEMPLATE/feature_request.yml +++ b/.github/ISSUE_TEMPLATE/feature_request.yml @@ -1,5 +1,5 @@ name: Feature request -description: Suggest an idea for the IntGenomicsLab/lr_somatic pipeline +description: Suggest an idea for the IntGenomicsLab/lrsomatic pipeline labels: enhancement body: - type: textarea diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md index 751e0d91..1e0906c0 100644 --- a/.github/PULL_REQUEST_TEMPLATE.md +++ b/.github/PULL_REQUEST_TEMPLATE.md @@ -1,21 +1,21 @@ ## PR checklist - [ ] This comment contains a description of changes (with reason). - [ ] If you've fixed a bug or added code that should be tested, add tests! -- [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/IntGenomicsLab/lr_somatic/tree/main/docs/CONTRIBUTING.md) +- [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/IntGenomicsLab/lrsomatic/tree/main/docs/CONTRIBUTING.md) - [ ] Make sure your code lints (`nf-core pipelines lint`). - [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --outdir `). - [ ] Check for unexpected warnings in debug mode (`nextflow run . -profile debug,test,docker --outdir `). diff --git a/.github/actions/nf-test/action.yml b/.github/actions/nf-test/action.yml index ad686e8e..4175e3c8 100644 --- a/.github/actions/nf-test/action.yml +++ b/.github/actions/nf-test/action.yml @@ -20,12 +20,12 @@ runs: using: "composite" steps: - name: Setup Nextflow - uses: nf-core/setup-nextflow@b4ec1bc7c16a94435159de94a05253542fddf6ef # v3 + uses: nf-core/setup-nextflow@893c28b667aedeba26e37f296d260ccc5bc4d914 # v3 with: version: "${{ env.NXF_VERSION }}" - name: Set up Python - uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6 + uses: actions/setup-python@5fda3b95a4ea91299a34e894583c3862153e4b97 # v7 with: python-version: "3.14" @@ -37,7 +37,7 @@ runs: - name: Setup apptainer if: contains(inputs.profile, 'singularity') - uses: eWaterCycle/setup-apptainer@3f706d898c9db585b1d741b4692e66755f3a1b40 # v2 + uses: eWaterCycle/setup-apptainer@3f706d898c9db585b1d741b4692e66755f3a1b40 # v2.0.0 - name: Set up Singularity if: contains(inputs.profile, 'singularity') diff --git a/.github/workflows/branch.yml b/.github/workflows/branch.yml index 7e776210..7626b4a5 100644 --- a/.github/workflows/branch.yml +++ b/.github/workflows/branch.yml @@ -2,45 +2,61 @@ name: nf-core branch protection # This workflow is triggered on PRs to `main`/`master` branch on the repository # It fails when someone tries to make a PR against the nf-core `main`/`master` branch instead of `dev` on: - pull_request_target: + pull_request: branches: - main - master +permissions: {} + jobs: test: runs-on: ubuntu-latest steps: # PRs to the nf-core repo main/master branch are only ok if coming from the nf-core repo `dev` or any `patch` branches - name: Check PRs - if: github.repository == 'IntGenomicsLab/lr_somatic' + if: github.repository == 'IntGenomicsLab/lrsomatic' + env: + HEAD_REPO: ${{ github.event.pull_request.head.repo.full_name }} run: | - { [[ ${{github.event.pull_request.head.repo.full_name }} == IntGenomicsLab/lr_somatic ]] && [[ $GITHUB_HEAD_REF == "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]] + { [[ "$HEAD_REPO" == IntGenomicsLab/lrsomatic ]] && [[ $GITHUB_HEAD_REF == "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]] - # If the above check failed, post a comment on the PR explaining the failure - # NOTE - this doesn't currently work if the PR is coming from a fork, due to limitations in GitHub actions secrets - - name: Post PR comment + # If the above check failed, build a comment to be posted by the shared poster workflow + - name: Build PR comment if: failure() - uses: mshick/add-pr-comment@8e4927817251f1ff60c001f04568532b38e0b4a0 # v3 - with: - message: | - ## This PR is against the `${{github.event.pull_request.base.ref}}` branch :x: + env: + PR_NUMBER: ${{ github.event.pull_request.number }} + BASE_REF: ${{ github.event.pull_request.base.ref }} + HEAD_REPO: ${{ github.event.pull_request.head.repo.full_name }} + PR_USER: ${{ github.event.pull_request.user.login }} + run: | + mkdir -p pr-comment + echo "$PR_NUMBER" > pr-comment/pr_number.txt + echo "branch" > pr-comment/header.txt + cat > pr-comment/comment.md <> "$GITHUB_OUTPUT" - name: Install dependencies run: | diff --git a/.github/workflows/fix_linting.yml b/.github/workflows/fix_linting.yml index 79b4bc3f..61394953 100644 --- a/.github/workflows/fix_linting.yml +++ b/.github/workflows/fix_linting.yml @@ -9,11 +9,11 @@ jobs: if: > contains(github.event.comment.html_url, '/pull/') && contains(github.event.comment.body, '@nf-core-bot fix linting') && - github.repository == 'IntGenomicsLab/lr_somatic' + github.repository == 'IntGenomicsLab/lrsomatic' runs-on: ubuntu-latest steps: # Use the @nf-core-bot token to check out so we can push later - - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6 + - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7 with: token: ${{ secrets.nf_core_bot_auth_token }} @@ -32,12 +32,12 @@ jobs: GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }} - name: Install Nextflow - uses: nf-core/setup-nextflow@b4ec1bc7c16a94435159de94a05253542fddf6ef # v3 + uses: nf-core/setup-nextflow@893c28b667aedeba26e37f296d260ccc5bc4d914 # v3 # Install and run prek - name: Run prek id: prek - uses: j178/prek-action@6ad80277337ad479fe43bd70701c3f7f8aa74db3 # v2 + uses: j178/prek-action@5337cb91e0fa35a7ff31b9ca345126d8bbbcdf16 # v2 continue-on-error: true # indication that the linting has finished @@ -82,4 +82,4 @@ jobs: issue-number: ${{ github.event.issue.number }} body: | @${{ github.actor }} I tried to fix the linting errors, but it didn't work. Please fix them manually. - See [CI log](https://github.com/IntGenomicsLab/lr_somatic/actions/runs/${{ github.run_id }}) for more details. + See [CI log](https://github.com/IntGenomicsLab/lrsomatic/actions/runs/${{ github.run_id }}) for more details. diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml index 8738ffc9..277f12fb 100644 --- a/.github/workflows/linting.yml +++ b/.github/workflows/linting.yml @@ -11,30 +11,30 @@ jobs: pre-commit: runs-on: ubuntu-latest steps: - - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6 + - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7 - name: Install Nextflow - uses: nf-core/setup-nextflow@b4ec1bc7c16a94435159de94a05253542fddf6ef # v3 + uses: nf-core/setup-nextflow@893c28b667aedeba26e37f296d260ccc5bc4d914 # v3 - name: Run prek - uses: j178/prek-action@6ad80277337ad479fe43bd70701c3f7f8aa74db3 # v2 + uses: j178/prek-action@5337cb91e0fa35a7ff31b9ca345126d8bbbcdf16 # v2 nf-core: runs-on: ubuntu-latest steps: - name: Check out pipeline code - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6 + uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7 - name: Install Nextflow - uses: nf-core/setup-nextflow@b4ec1bc7c16a94435159de94a05253542fddf6ef # v3 + uses: nf-core/setup-nextflow@893c28b667aedeba26e37f296d260ccc5bc4d914 # v3 - - uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6 + - uses: actions/setup-python@5fda3b95a4ea91299a34e894583c3862153e4b97 # v7 with: python-version: "3.14" architecture: "x64" - name: Setup uv - uses: astral-sh/setup-uv@08807647e7069bb48b6ef5acd8ec9567f424441b # v8.1.0 + uses: astral-sh/setup-uv@c771a70e6277c0a99b617c7a806ffedaca235ff9 # v9.0.0 - name: read .nf-core.yml uses: pietrobolcato/action-read-yaml@9f13718d61111b69f30ab4ac683e67a56d254e1d # 1.1.0 @@ -46,7 +46,7 @@ jobs: run: uv tool install nf-core==${{ steps.read_yml.outputs['nf_core_version'] }} - name: Run nf-core pipelines lint - if: ${{ github.base_ref != 'master' || github.base_ref != 'main' }} + if: ${{ github.base_ref != 'master' && github.base_ref != 'main' }} env: GITHUB_COMMENTS_URL: ${{ github.event.pull_request.comments_url }} GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} @@ -74,3 +74,21 @@ jobs: lint_log.txt lint_results.md PR_number.txt + + # Build a comment for the shared pr-comment.yml poster to publish on the PR + - name: Prepare PR comment + if: ${{ always() }} + env: + PR_NUMBER: ${{ github.event.pull_request.number }} + run: | + mkdir -p pr-comment + echo "$PR_NUMBER" > pr-comment/pr_number.txt + echo "lint" > pr-comment/header.txt + [ -f lint_results.md ] && cp lint_results.md pr-comment/comment.md || true + + - name: Upload PR comment artifact + if: ${{ always() }} + uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7 + with: + name: pr-comment + path: pr-comment/ diff --git a/.github/workflows/nf-test.yml b/.github/workflows/nf-test.yml index 3a48a15b..3dc798a8 100644 --- a/.github/workflows/nf-test.yml +++ b/.github/workflows/nf-test.yml @@ -39,7 +39,7 @@ jobs: rm -rf ./* || true rm -rf ./.??* || true ls -la ./ - - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6 + - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7 with: fetch-depth: 0 @@ -83,7 +83,7 @@ jobs: TOTAL_SHARDS: ${{ needs.nf-test-changes.outputs.total_shards }} steps: - - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6 + - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7 with: fetch-depth: 0 @@ -114,6 +114,22 @@ jobs: fi fi + # continue-on-error keeps latest-everything from failing the job, so it never shows up in + # `needs.nf-test.result` downstream and CI stays green. Surface it via a PR comment instead; + # other NXF_VER failures already fail the job/CI directly, so no comment is needed for those. + - name: Prepare PR comment fragment + if: ${{ always() && steps.run_nf_test.outcome == 'failure' && matrix.NXF_VER == 'latest-everything' }} + run: | + mkdir -p pr-comment-fragment + echo "* ❌ \`${{ matrix.profile }}\` | \`${{ matrix.NXF_VER }}\` | Shard ${{ matrix.shard }}/${{ env.TOTAL_SHARDS }}" > pr-comment-fragment/fragment.md + + - name: Upload PR comment fragment + if: ${{ always() && steps.run_nf_test.outcome == 'failure' && matrix.NXF_VER == 'latest-everything' }} + uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7 + with: + name: pr-comment-fragment-${{ strategy.job-index }} + path: pr-comment-fragment/ + confirm-pass: needs: [nf-test] if: always() @@ -139,3 +155,44 @@ jobs: echo "DEBUG: toJSON(needs) = ${{ toJSON(needs) }}" echo "DEBUG: toJSON(needs.*.result) = ${{ toJSON(needs.*.result) }}" echo "::endgroup::" + + - name: Download PR comment fragments + if: ${{ always() }} + uses: actions/download-artifact@3e5f45b2cfb9172054b4087a40e8e0b5a5461e7c # v8.0.1 + continue-on-error: true + with: + pattern: pr-comment-fragment-* + path: pr-comment-fragments + merge-multiple: true + + # Build a comment for the shared pr-comment.yml poster to publish on the PR. + # Based on the fragments above (not needs.*.result) so non-blocking failures are still reported. + - name: Prepare PR comment + if: ${{ always() }} + env: + PR_NUMBER: ${{ github.event.pull_request.number }} + RUN_URL: ${{ github.server_url }}/${{ github.repository }}/actions/runs/${{ github.run_id }} + run: | + mkdir -p pr-comment + echo "$PR_NUMBER" > pr-comment/pr_number.txt + echo "nf-test" > pr-comment/header.txt + if [ -d pr-comment-fragments ] && [ -n "$(ls -A pr-comment-fragments)" ]; then + { + echo "## ❌ nf-test failed with latest Nextflow version" + echo "" + echo "> [!NOTE]" + echo "> Tests with Nextflow's latest version failed but it will not cause a CI workflow failure." + echo "> Please check if the failure is expected with newer (edge-)releases of Nextflow or if it needs fixing." + echo "" + cat pr-comment-fragments/*.md + echo "" + echo "See the [full run](${RUN_URL}) for details." + } > pr-comment/comment.md + fi + + - name: Upload PR comment artifact + if: ${{ always() }} + uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7 + with: + name: pr-comment + path: pr-comment/ diff --git a/.github/workflows/pr-comment.yml b/.github/workflows/pr-comment.yml new file mode 100644 index 00000000..ab7b59dd --- /dev/null +++ b/.github/workflows/pr-comment.yml @@ -0,0 +1,82 @@ +name: Post PR comment +# Shared, privileged comment poster. +# +# This is the single workflow that runs with a write token. It is triggered +# after any of the listed "producer" workflows complete on a pull request. +# Each producer runs untrusted PR code (if any) with a read-only token and +# uploads a `pr-comment` artifact describing the comment to post; this workflow +# only ever reads that plain-text artifact, so no PR code is executed here. +# +# Artifact contract (uploaded by producers under the name `pr-comment`): +# pr_number.txt - the pull request number +# header.txt - sticky-comment identifier (keeps comment types separate) +# comment.md - the Markdown body (omit the file to post nothing) + +on: + workflow_run: + workflows: + - "nf-core linting" + - "nf-core template version comment" + - "nf-core branch protection" + - "Run nf-test" + +permissions: + actions: read + contents: read + pull-requests: write + +jobs: + post-comment: + runs-on: ubuntu-latest + if: github.event.workflow_run.event == 'pull_request' + steps: + - name: Download PR comment artifact + uses: dawidd6/action-download-artifact@b6e2e70617bc3265edd6dab6c906732b2f1ae151 # v21 + with: + run_id: ${{ github.event.workflow_run.id }} + name: pr-comment + path: pr-comment + if_no_artifact_found: ignore + + - name: Read comment metadata + id: meta + run: | + echo "::group::Downloaded pr-comment contents" + ls -la pr-comment 2>/dev/null || echo "No pr-comment/ directory was downloaded." + echo "::endgroup::" + + if [ ! -d pr-comment ]; then + echo "No pr-comment artifact found; nothing to post." + exit 0 + fi + + if [ ! -f pr-comment/comment.md ]; then + echo "Artifact present but no comment.md; nothing to post." + exit 0 + fi + + pr_number=$(cat pr-comment/pr_number.txt) + header=$(cat pr-comment/header.txt) + echo "Found comment.md (header='$header', pr_number='$pr_number')." + + # Guard against anything unexpected ending up in the PR number. + case "$pr_number" in + ''|*[!0-9]*) + echo "Invalid PR number: '$pr_number'" + exit 1 + ;; + esac + + echo "pr_number=$pr_number" >> "$GITHUB_OUTPUT" + echo "header=$header" >> "$GITHUB_OUTPUT" + echo "post=true" >> "$GITHUB_OUTPUT" + echo "Will post comment to PR #${pr_number}." + + - name: Post PR comment + if: steps.meta.outputs.post == 'true' + uses: marocchino/sticky-pull-request-comment@5770ad5eb8f42dd2c4f34da00c94c5381e49af88 # v3.0.5 + with: + GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} + number: ${{ steps.meta.outputs.pr_number }} + header: ${{ steps.meta.outputs.header }} + path: pr-comment/comment.md diff --git a/.github/workflows/template-version-comment.yml b/.github/workflows/template-version-comment.yml index ea30827e..149e2851 100644 --- a/.github/workflows/template-version-comment.yml +++ b/.github/workflows/template-version-comment.yml @@ -2,14 +2,17 @@ name: nf-core template version comment # This workflow is triggered on PRs to check if the pipeline template version matches the latest nf-core version. # It posts a comment to the PR, even if it comes from a fork. -on: pull_request_target +on: + pull_request: + +permissions: {} jobs: - template_version: + check_template_version: runs-on: ubuntu-latest steps: - name: Check out pipeline code - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6 + uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7 with: ref: ${{ github.event.pull_request.head.sha }} @@ -22,25 +25,36 @@ jobs: - name: Install nf-core run: | python -m pip install --upgrade pip - pip install nf-core==${{ steps.read_yml.outputs['nf_core_version'] }} + pip install nf-core + + - name: Build PR comment if template is outdated + # The fork-controlled version is passed via the environment and only ever + # used as quoted shell data (never interpolated into a command), so it + # cannot be used for script injection. + env: + PR_VERSION: ${{ steps.read_yml.outputs['nf_core_version'] }} + PR_NUMBER: ${{ github.event.pull_request.number }} + run: | + mkdir -p pr-comment + echo "$PR_NUMBER" > pr-comment/pr_number.txt + echo "template-version" > pr-comment/header.txt + + latest_version=$(nf-core --version | grep -oE '[0-9]+\.[0-9]+\.[0-9]+' | head -n1) - - name: Check nf-core outdated - id: nf_core_outdated - run: echo "OUTPUT=$(pip list --outdated | grep nf-core)" >> ${GITHUB_ENV} + if [ -n "$PR_VERSION" ] && [ -n "$latest_version" ] && [ "$PR_VERSION" != "$latest_version" ]; then + cat > pr-comment/comment.md < [!WARNING] + > Newer version of the nf-core template is available. + > + > Your pipeline is using an old version of the nf-core template: ${PR_VERSION}. + > Please update your pipeline to the latest version. + > + > For more documentation on how to update your pipeline, please see the [Synchronisation documentation](https://nf-co.re/docs/developing/template-syncs/overview). + EOF + fi - - name: Post nf-core template version comment - uses: mshick/add-pr-comment@8e4927817251f1ff60c001f04568532b38e0b4a0 # v3 - if: | - contains(env.OUTPUT, 'nf-core') + - name: Upload PR comment artifact + uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7 with: - repo-token: ${{ secrets.NF_CORE_BOT_AUTH_TOKEN }} - allow-repeats: false - message: | - > [!WARNING] - > Newer version of the nf-core template is available. - > - > Your pipeline is using an old version of the nf-core template: ${{ steps.read_yml.outputs['nf_core_version'] }}. - > Please update your pipeline to the latest version. - > - > For more documentation on how to update your pipeline, please see the [Synchronisation documentation](https://nf-co.re/docs/developing/template-syncs/overview). - # + name: pr-comment + path: pr-comment/ diff --git a/.hooks/block_pipeline_outdir.sh b/.hooks/block_pipeline_outdir.sh new file mode 100755 index 00000000..e9ba4f93 --- /dev/null +++ b/.hooks/block_pipeline_outdir.sh @@ -0,0 +1,44 @@ +#!/usr/bin/env bash +# This hook is used to block commits if they include staged files inside a directory +# which also contains a subdirectory called `pipeline_info`. The purpose of this is to +# prevent users from inadvertently committing output from pipeline test runs inside the +# development directory. + +set -e + +status=0 +seen_dirs="" + +while IFS= read -r file; do + # The offending output bundle's root is the ancestor directory that has + # `pipeline_info` as an immediate child, so callers can restore it in one go. + if [[ "$file" == pipeline_info/* ]]; then + top_dir="pipeline_info" + elif [[ "$file" == */pipeline_info/* ]]; then + top_dir="${file%%/pipeline_info/*}" + else + top_dir="" + dir=$(dirname "$file") + while [[ "$dir" != "." && "$dir" != "/" ]]; do + if [[ -d "$dir/pipeline_info" ]]; then + top_dir="$dir" + break + fi + dir=$(dirname "$dir") + done + fi + + if [[ -n "$top_dir" ]]; then + echo "❌ Commit blocked: Please do not commit output from pipeline test runs to the pipeline code itself: $file" + status=1 + case "$seen_dirs" in + *"|$top_dir|"*) ;; + *) + echo "Run 'git restore --staged $top_dir' to remove the whole output folder from the staging area." + seen_dirs="$seen_dirs|$top_dir|" + ;; + esac + fi +done < <(git diff --cached --name-only) + +exit "$status" diff --git a/.nf-core.yml b/.nf-core.yml index 1d6da6cf..0caf039c 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -1,22 +1,26 @@ lint: files_exist: - CODE_OF_CONDUCT.md - - assets/nf-core-lr_somatic_logo_light.png - - docs/images/nf-core-lr_somatic_logo_light.png - - docs/images/nf-core-lr_somatic_logo_dark.png + - assets/nf-core-lrsomatic_logo_light.png + - docs/images/nf-core-lrsomatic_logo_light.png + - docs/images/nf-core-lrsomatic_logo_dark.png - .github/ISSUE_TEMPLATE/config.yml - .github/workflows/awstest.yml - .github/workflows/awsfulltest.yml + - .github/CONTRIBUTING.md files_unchanged: - CODE_OF_CONDUCT.md - - assets/nf-core-lr_somatic_logo_light.png - - docs/images/nf-core-lr_somatic_logo_light.png - - docs/images/nf-core-lr_somatic_logo_dark.png + - assets/nf-core-lrsomatic_logo_light.png + - docs/images/nf-core-lrsomatic_logo_light.png + - docs/images/nf-core-lrsomatic_logo_dark.png - .github/ISSUE_TEMPLATE/bug_report.yml - .github/CONTRIBUTING.md - .github/PULL_REQUEST_TEMPLATE.md - assets/email_template.txt - docs/README.md + - .github/workflows/branch.yml + - .github/workflows/linting_comment.yml + - .github/workflows/linting.yml multiqc_config: - report_comment nextflow_config: @@ -26,16 +30,16 @@ lint: - validation.help.afterText - validation.summary.beforeText - validation.summary.afterText -nf_core_version: 4.0.1 +nf_core_version: 4.1.0 repository_type: pipeline template: - author: Jonas Demeulemeester + author: Robert Forsyth & Luuk Harbers description: Workflow for somatic variant calling of long read data force: false is_nfcore: false - name: lr_somatic + name: lrsomatic org: IntGenomicsLab outdir: . skip_features: - fastqc - version: 1.0.0dev + version: 1.1.0 diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index f51e1a28..e9503db1 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -4,7 +4,7 @@ repos: hooks: - id: prettier additional_dependencies: - - prettier@3.8.3 + - prettier@3.9.6 - repo: https://github.com/pre-commit/pre-commit-hooks rev: v6.0.0 hooks: @@ -25,9 +25,26 @@ repos: subworkflows/(?!local/).*| .*\.snap$ )$ + - id: check-added-large-files + args: [--maxkb=5000] + exclude: | + (?x)^( + .*ro-crate-metadata.json$| + .*\.snap$| + lib/nfcore_external_java_deps.jar$| + docs/.*\.(svg|pdf)$| + assets/.*$ + )$ + - id: check-merge-conflict - repo: https://github.com/seqeralabs/nf-lint-pre-commit rev: v0.3.0 hooks: - id: nextflow-lint files: '\.nf$|nextflow\.config$' args: ["-output", "json"] + - repo: local + hooks: + - id: block-pipeline-outdir + name: Prevent committing output from pipeline test runs to the pipeline code itself + entry: ./.hooks/block_pipeline_outdir.sh + language: script diff --git a/CHANGELOG.md b/CHANGELOG.md index ee035dca..c8994969 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,11 +1,11 @@ -# IntGenomicsLab/lr_somatic: Changelog +# IntGenomicsLab/lrsomatic: Changelog 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). -## v1.0.0dev - [date] +## v1.1.0 - [unreleased] -Initial release of IntGenomicsLab/lr_somatic, created with the [nf-core](https://nf-co.re/) template. +Initial release of IntGenomicsLab/lrsomatic, created with the [nf-core](https://nf-co.re/) template. ### `Added` diff --git a/CITATIONS.md b/CITATIONS.md index 08105ad6..33c9f5f1 100644 --- a/CITATIONS.md +++ b/CITATIONS.md @@ -1,4 +1,4 @@ -# IntGenomicsLab/lr_somatic: Citations +# IntGenomicsLab/lrsomatic: Citations ## [nf-core](https://pubmed.ncbi.nlm.nih.gov/32055031/) diff --git a/LICENSE b/LICENSE index 21de0ec6..27d3cdc5 100644 --- a/LICENSE +++ b/LICENSE @@ -1,6 +1,6 @@ MIT License -Copyright (c) The IntGenomicsLab/lr_somatic team +Copyright (c) The IntGenomicsLab/lrsomatic team Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal diff --git a/README.md b/README.md index 024ef140..edd145d8 100644 --- a/README.md +++ b/README.md @@ -1,20 +1,20 @@ -# IntGenomicsLab/lr_somatic +# IntGenomicsLab/lrsomatic -[![Open in GitHub Codespaces](https://img.shields.io/badge/Open_In_GitHub_Codespaces-black?labelColor=grey&logo=github)](https://github.com/codespaces/new/IntGenomicsLab/lr_somatic) -[![GitHub Actions CI Status](https://github.com/IntGenomicsLab/lr_somatic/actions/workflows/nf-test.yml/badge.svg)](https://github.com/IntGenomicsLab/lr_somatic/actions/workflows/nf-test.yml) -[![GitHub Actions Linting Status](https://github.com/IntGenomicsLab/lr_somatic/actions/workflows/linting.yml/badge.svg)](https://github.com/IntGenomicsLab/lr_somatic/actions/workflows/linting.yml)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX) +[![Open in GitHub Codespaces](https://img.shields.io/badge/Open_In_GitHub_Codespaces-black?labelColor=grey&logo=github)](https://github.com/codespaces/new/IntGenomicsLab/lrsomatic) +[![GitHub Actions CI Status](https://github.com/IntGenomicsLab/lrsomatic/actions/workflows/nf-test.yml/badge.svg)](https://github.com/IntGenomicsLab/lrsomatic/actions/workflows/nf-test.yml) +[![GitHub Actions Linting Status](https://github.com/IntGenomicsLab/lrsomatic/actions/workflows/linting.yml/badge.svg)](https://github.com/IntGenomicsLab/lrsomatic/actions/workflows/linting.yml)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX) [![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com) [![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.10.4-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/) -[![nf-core template version](https://img.shields.io/badge/nf--core_template-4.0.1-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/4.0.1) +[![nf-core template version](https://img.shields.io/badge/nf--core_template-4.1.0-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/4.1.0) [![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/) [![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/) [![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/) -[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/IntGenomicsLab/lr_somatic) +[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/IntGenomicsLab/lrsomatic) ## Introduction -**IntGenomicsLab/lr_somatic** is a bioinformatics pipeline that ... +**IntGenomicsLab/lrsomatic** is a bioinformatics pipeline that ... ```bash -nextflow run IntGenomicsLab/lr_somatic \ +nextflow run IntGenomicsLab/lrsomatic \ -profile \ --input samplesheet.csv \ --outdir @@ -63,7 +63,7 @@ nextflow run IntGenomicsLab/lr_somatic \ ## Credits -IntGenomicsLab/lr_somatic was originally written by Jonas Demeulemeester. +IntGenomicsLab/lrsomatic was originally written by Robert Forsyth & Luuk Harbers. We thank the following people for their extensive assistance in the development of this pipeline: @@ -76,7 +76,7 @@ If you would like to contribute to this pipeline, please see the [contributing g ## Citations - + diff --git a/assets/email_template.html b/assets/email_template.html index 43e12a3f..f1b77923 100644 --- a/assets/email_template.html +++ b/assets/email_template.html @@ -4,21 +4,21 @@ - - IntGenomicsLab/lr_somatic Pipeline Report + + IntGenomicsLab/lrsomatic Pipeline Report
-

IntGenomicsLab/lr_somatic ${version}

+

IntGenomicsLab/lrsomatic ${version}

Run Name: $runName

<% if (!success){ out << """
-

IntGenomicsLab/lr_somatic execution completed unsuccessfully!

+

IntGenomicsLab/lrsomatic execution completed unsuccessfully!

The exit status of the task that caused the workflow execution to fail was: $exitStatus.

The full error message was:

${errorReport}
@@ -27,7 +27,7 @@

IntGenomicsLab/lr_somatic execution co } else { out << """
- IntGenomicsLab/lr_somatic execution completed successfully! + IntGenomicsLab/lrsomatic execution completed successfully!
""" } @@ -44,8 +44,8 @@

Pipeline Configuration:

-

IntGenomicsLab/lr_somatic

-

https://github.com/IntGenomicsLab/lr_somatic

+

IntGenomicsLab/lrsomatic

+

https://github.com/IntGenomicsLab/lrsomatic

diff --git a/assets/email_template.txt b/assets/email_template.txt index 95bc07e2..ceaf72dd 100644 --- a/assets/email_template.txt +++ b/assets/email_template.txt @@ -1,10 +1,10 @@ Run Name: $runName <% if (success){ - out << "## IntGenomicsLab/lr_somatic execution completed successfully! ##" + out << "## IntGenomicsLab/lrsomatic execution completed successfully! ##" } else { out << """#################################################### -## IntGenomicsLab/lr_somatic execution completed unsuccessfully! ## +## IntGenomicsLab/lrsomatic execution completed unsuccessfully! ## #################################################### The exit status of the task that caused the workflow execution to fail was: $exitStatus. The full error message was: @@ -27,5 +27,5 @@ Pipeline Configuration: <% out << summary.collect{ k,v -> " - $k: $v" }.join("\n") %> -- -IntGenomicsLab/lr_somatic -https://github.com/IntGenomicsLab/lr_somatic +IntGenomicsLab/lrsomatic +https://github.com/IntGenomicsLab/lrsomatic diff --git a/assets/methods_description_template.yml b/assets/methods_description_template.yml index 2ec82a50..fca23d8a 100644 --- a/assets/methods_description_template.yml +++ b/assets/methods_description_template.yml @@ -1,13 +1,13 @@ -id: "IntGenomicsLab-lr_somatic-methods-description" +id: "IntGenomicsLab-lrsomatic-methods-description" description: "Suggested text and references to use when describing pipeline usage within the methods section of a publication." -section_name: "IntGenomicsLab/lr_somatic Methods Description" -section_href: "https://github.com/IntGenomicsLab/lr_somatic" +section_name: "IntGenomicsLab/lrsomatic Methods Description" +section_href: "https://github.com/IntGenomicsLab/lrsomatic" plot_type: "html" ## TODO nf-core: Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline ## You inject any metadata in the Nextflow '${workflow}' object data: |

Methods

-

Data was processed using IntGenomicsLab/lr_somatic v${workflow.manifest.version} ${doi_text} of the nf-core collection of workflows (Ewels et al., 2020), utilising reproducible software environments from the Bioconda (Grüning et al., 2018) and Biocontainers (da Veiga Leprevost et al., 2017) projects.

+

Data was processed using IntGenomicsLab/lrsomatic v${workflow.manifest.version} ${doi_text} of the nf-core collection of workflows (Ewels et al., 2020), utilising reproducible software environments from the Bioconda (Grüning et al., 2018) and Biocontainers (da Veiga Leprevost et al., 2017) projects.

The pipeline was executed with Nextflow v${workflow.nextflow.version} (Di Tommaso et al., 2017) with the following command:

${workflow.commandLine}

${tool_citations}

diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index d1ad8766..c24ed9ed 100644 --- a/assets/multiqc_config.yml +++ b/assets/multiqc_config.yml @@ -1,12 +1,12 @@ report_comment: > - This report has been generated by the IntGenomicsLab/lr_somatic + This report has been generated by the IntGenomicsLab/lrsomatic analysis pipeline. report_section_order: - "IntGenomicsLab-lr_somatic-methods-description": + "IntGenomicsLab-lrsomatic-methods-description": order: -1000 software_versions: order: -1001 - "IntGenomicsLab-lr_somatic-summary": + "IntGenomicsLab-lrsomatic-summary": order: -1002 export_plots: true diff --git a/assets/schema_input.json b/assets/schema_input.json index f35055e5..fb9acd00 100644 --- a/assets/schema_input.json +++ b/assets/schema_input.json @@ -1,7 +1,7 @@ { "$schema": "https://json-schema.org/draft/2020-12/schema", - "$id": "https://raw.githubusercontent.com/IntGenomicsLab/lr_somatic/main/assets/schema_input.json", - "title": "IntGenomicsLab/lr_somatic pipeline - params.input schema", + "$id": "https://raw.githubusercontent.com/IntGenomicsLab/lrsomatic/main/assets/schema_input.json", + "title": "IntGenomicsLab/lrsomatic pipeline - params.input schema", "description": "Schema for the file provided with params.input", "type": "array", "items": { diff --git a/assets/sendmail_template.txt b/assets/sendmail_template.txt index 831121de..2e397d1b 100644 --- a/assets/sendmail_template.txt +++ b/assets/sendmail_template.txt @@ -9,12 +9,12 @@ Content-Type: text/html; charset=utf-8 $email_html --nfcoremimeboundary -Content-Type: image/png;name="IntGenomicsLab-lr_somatic_logo.png" +Content-Type: image/png;name="IntGenomicsLab-lrsomatic_logo.png" Content-Transfer-Encoding: base64 Content-ID: -Content-Disposition: inline; filename="IntGenomicsLab-lr_somatic_logo_light.png" +Content-Disposition: inline; filename="IntGenomicsLab-lrsomatic_logo_light.png" -<% out << new File("$projectDir/assets/IntGenomicsLab-lr_somatic_logo_light.png"). +<% out << new File("$projectDir/assets/IntGenomicsLab-lrsomatic_logo_light.png"). bytes. encodeBase64(). toString(). diff --git a/conf/base.config b/conf/base.config index 568e8a4e..40eeb06a 100644 --- a/conf/base.config +++ b/conf/base.config @@ -1,6 +1,6 @@ /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - IntGenomicsLab/lr_somatic Nextflow base config file + IntGenomicsLab/lrsomatic Nextflow base config file ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ A 'blank slate' config file, appropriate for general use on most high performance compute environments. Assumes that all software is installed and available on @@ -49,6 +49,9 @@ process { withLabel:process_long { time = { 20.h * task.attempt } } + withLabel:process_low_memory { + memory = { 1.GB * task.attempt } + } withLabel:process_high_memory { memory = { 200.GB * task.attempt } } diff --git a/conf/containers_conda_lock_files_amd64.config b/conf/containers_conda_lock_files_amd64.config index f487ba40..eb32fe50 100644 --- a/conf/containers_conda_lock_files_amd64.config +++ b/conf/containers_conda_lock_files_amd64.config @@ -1 +1 @@ -process { withName: 'MULTIQC' { container = 'modules/nf-core/multiqc/.conda-lock/linux_amd64-bd-db7c73dae76bc9e6_1.txt' } } +process { withName: 'MULTIQC' { conda = 'modules/nf-core/multiqc/.conda-lock/linux_amd64-bd-c17fb751507e9dfc_1.txt' } } diff --git a/conf/containers_conda_lock_files_arm64.config b/conf/containers_conda_lock_files_arm64.config index e9a3fedc..3733ddfd 100644 --- a/conf/containers_conda_lock_files_arm64.config +++ b/conf/containers_conda_lock_files_arm64.config @@ -1 +1 @@ -process { withName: 'MULTIQC' { container = 'modules/nf-core/multiqc/.conda-lock/linux_arm64-bd-d167b8012595a136_1.txt' } } +process { withName: 'MULTIQC' { conda = 'modules/nf-core/multiqc/.conda-lock/linux_arm64-bd-5c84a5000a226ab5_1.txt' } } diff --git a/conf/containers_docker_amd64.config b/conf/containers_docker_amd64.config index 01b59df5..ea18c3f9 100644 --- a/conf/containers_docker_amd64.config +++ b/conf/containers_docker_amd64.config @@ -1 +1 @@ -process { withName: 'MULTIQC' { container = 'community.wave.seqera.io/library/multiqc:1.34--db7c73dae76bc9e6' } } +process { withName: 'MULTIQC' { container = 'community.wave.seqera.io/library/multiqc:1.35--c17fb751507e9dfc' } } diff --git a/conf/containers_docker_arm64.config b/conf/containers_docker_arm64.config index 7785cb13..369f743a 100644 --- a/conf/containers_docker_arm64.config +++ b/conf/containers_docker_arm64.config @@ -1 +1 @@ -process { withName: 'MULTIQC' { container = 'community.wave.seqera.io/library/multiqc:1.34--d167b8012595a136' } } +process { withName: 'MULTIQC' { container = 'community.wave.seqera.io/library/multiqc:1.35--5c84a5000a226ab5' } } diff --git a/conf/containers_singularity_https_amd64.config b/conf/containers_singularity_https_amd64.config index 754821b3..932fc7c0 100644 --- a/conf/containers_singularity_https_amd64.config +++ b/conf/containers_singularity_https_amd64.config @@ -1 +1 @@ -process { withName: 'MULTIQC' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/1b/1bef8af6be88c5733461959c46ac8ef73d18f65277f62a1695d0e1633054f9c2/data' } } +process { withName: 'MULTIQC' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/c8/c8e346f4f6080eadf1253505e6ff09ef004454fc18e8d672006fd7b222cc412e/data' } } diff --git a/conf/containers_singularity_https_arm64.config b/conf/containers_singularity_https_arm64.config index 93071de8..4f795323 100644 --- a/conf/containers_singularity_https_arm64.config +++ b/conf/containers_singularity_https_arm64.config @@ -1 +1 @@ -process { withName: 'MULTIQC' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/9a/9a1fec9662a152683e6fcae440d0ce20920b3b89dc62d1e3a52e73f92eba0969/data' } } +process { withName: 'MULTIQC' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/e4/e48aa28aebc881254a499b24c3e1ce77b8df1b85a5432699ed6f72eb17ac7fb5/data' } } diff --git a/conf/containers_singularity_oras_amd64.config b/conf/containers_singularity_oras_amd64.config index 952881d8..2fa065b3 100644 --- a/conf/containers_singularity_oras_amd64.config +++ b/conf/containers_singularity_oras_amd64.config @@ -1 +1 @@ -process { withName: 'MULTIQC' { container = 'oras://community.wave.seqera.io/library/multiqc:1.34--4fc8657c816047c0' } } +process { withName: 'MULTIQC' { container = 'oras://community.wave.seqera.io/library/multiqc:1.35--c680f2aea25ccec2' } } diff --git a/conf/containers_singularity_oras_arm64.config b/conf/containers_singularity_oras_arm64.config index 498ec506..84f07924 100644 --- a/conf/containers_singularity_oras_arm64.config +++ b/conf/containers_singularity_oras_arm64.config @@ -1 +1 @@ -process { withName: 'MULTIQC' { container = 'oras://community.wave.seqera.io/library/multiqc:1.34--7fbd82d945c06726' } } +process { withName: 'MULTIQC' { container = 'oras://community.wave.seqera.io/library/multiqc:1.35--c0468833d65b2f81' } } diff --git a/conf/igenomes.config b/conf/igenomes.config index 3f114377..b8c8154e 100644 --- a/conf/igenomes.config +++ b/conf/igenomes.config @@ -8,433 +8,431 @@ ---------------------------------------------------------------------------------------- */ -params { +params.genomes = [ // illumina iGenomes reference file paths - genomes { - 'GRCh37' { - fasta = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Annotation/README.txt" - mito_name = "MT" - macs_gsize = "2.7e9" - blacklist = "${projectDir}/assets/blacklists/GRCh37-blacklist.bed" - } - 'GRCh38' { - fasta = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Annotation/Genes/genes.bed" - mito_name = "chrM" - macs_gsize = "2.7e9" - blacklist = "${projectDir}/assets/blacklists/hg38-blacklist.bed" - } - 'CHM13' { - fasta = "${params.igenomes_base}/Homo_sapiens/UCSC/CHM13/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Homo_sapiens/UCSC/CHM13/Sequence/BWAIndex/" - bwamem2 = "${params.igenomes_base}/Homo_sapiens/UCSC/CHM13/Sequence/BWAmem2Index/" - gtf = "${params.igenomes_base}/Homo_sapiens/NCBI/CHM13/Annotation/Genes/genes.gtf" - gff = "ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/009/914/755/GCF_009914755.1_T2T-CHM13v2.0/GCF_009914755.1_T2T-CHM13v2.0_genomic.gff.gz" - mito_name = "chrM" - } - 'GRCm38' { - fasta = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Annotation/README.txt" - mito_name = "MT" - macs_gsize = "1.87e9" - blacklist = "${projectDir}/assets/blacklists/GRCm38-blacklist.bed" - } - 'TAIR10' { - fasta = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Annotation/README.txt" - mito_name = "Mt" - } - 'EB2' { - fasta = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Annotation/README.txt" - } - 'UMD3.1' { - fasta = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Annotation/README.txt" - mito_name = "MT" - } - 'WBcel235' { - fasta = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Annotation/Genes/genes.bed" - mito_name = "MtDNA" - macs_gsize = "9e7" - } - 'CanFam3.1' { - fasta = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Annotation/README.txt" - mito_name = "MT" - } - 'GRCz10' { - fasta = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Annotation/Genes/genes.bed" - mito_name = "MT" - } - 'BDGP6' { - fasta = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Annotation/Genes/genes.bed" - mito_name = "M" - macs_gsize = "1.2e8" - } - 'EquCab2' { - fasta = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Annotation/README.txt" - mito_name = "MT" - } - 'EB1' { - fasta = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Annotation/README.txt" - } - 'Galgal4' { - fasta = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Annotation/Genes/genes.bed" - mito_name = "MT" - } - 'Gm01' { - fasta = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Annotation/README.txt" - } - 'Mmul_1' { - fasta = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Annotation/README.txt" - mito_name = "MT" - } - 'IRGSP-1.0' { - fasta = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Annotation/Genes/genes.bed" - mito_name = "Mt" - } - 'CHIMP2.1.4' { - fasta = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Annotation/README.txt" - mito_name = "MT" - } - 'Rnor_5.0' { - fasta = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Annotation/Genes/genes.bed" - mito_name = "MT" - } - 'Rnor_6.0' { - fasta = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Annotation/Genes/genes.bed" - mito_name = "MT" - } - 'R64-1-1' { - fasta = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Annotation/Genes/genes.bed" - mito_name = "MT" - macs_gsize = "1.2e7" - } - 'EF2' { - fasta = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Annotation/README.txt" - mito_name = "MT" - macs_gsize = "1.21e7" - } - 'Sbi1' { - fasta = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Annotation/README.txt" - } - 'Sscrofa10.2' { - fasta = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Annotation/README.txt" - mito_name = "MT" - } - 'AGPv3' { - fasta = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Annotation/Genes/genes.bed" - mito_name = "Mt" - } - 'hg38' { - fasta = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Annotation/Genes/genes.bed" - mito_name = "chrM" - macs_gsize = "2.7e9" - blacklist = "${projectDir}/assets/blacklists/hg38-blacklist.bed" - } - 'hg19' { - fasta = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Annotation/README.txt" - mito_name = "chrM" - macs_gsize = "2.7e9" - blacklist = "${projectDir}/assets/blacklists/hg19-blacklist.bed" - } - 'mm10' { - fasta = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Annotation/README.txt" - mito_name = "chrM" - macs_gsize = "1.87e9" - blacklist = "${projectDir}/assets/blacklists/mm10-blacklist.bed" - } - 'bosTau8' { - fasta = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Annotation/Genes/genes.bed" - mito_name = "chrM" - } - 'ce10' { - fasta = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Annotation/README.txt" - mito_name = "chrM" - macs_gsize = "9e7" - } - 'canFam3' { - fasta = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Annotation/README.txt" - mito_name = "chrM" - } - 'danRer10' { - fasta = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Annotation/Genes/genes.bed" - mito_name = "chrM" - macs_gsize = "1.37e9" - } - 'dm6' { - fasta = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Annotation/Genes/genes.bed" - mito_name = "chrM" - macs_gsize = "1.2e8" - } - 'equCab2' { - fasta = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Annotation/README.txt" - mito_name = "chrM" - } - 'galGal4' { - fasta = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Annotation/README.txt" - mito_name = "chrM" - } - 'panTro4' { - fasta = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Annotation/README.txt" - mito_name = "chrM" - } - 'rn6' { - fasta = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Annotation/Genes/genes.bed" - mito_name = "chrM" - } - 'sacCer3' { - fasta = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/BismarkIndex/" - readme = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Annotation/README.txt" - mito_name = "chrM" - macs_gsize = "1.2e7" - } - 'susScr3' { - fasta = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Annotation/README.txt" - mito_name = "chrM" - } - } -} + 'GRCh37' : [ + fasta : "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/WholeGenomeFasta/genome.fa", + bwa : "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/BWAIndex/version0.6.0/", + bowtie2 : "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/Bowtie2Index/", + star : "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/STARIndex/", + bismark : "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/BismarkIndex/", + gtf : "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Annotation/Genes/genes.gtf", + bed12 : "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Annotation/Genes/genes.bed", + readme : "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Annotation/README.txt", + mito_name : "MT", + macs_gsize : "2.7e9", + blacklist : "${projectDir}/assets/blacklists/GRCh37-blacklist.bed", + ], + 'GRCh38' : [ + fasta : "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/WholeGenomeFasta/genome.fa", + bwa : "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/BWAIndex/version0.6.0/", + bowtie2 : "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/Bowtie2Index/", + star : "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/STARIndex/", + bismark : "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/BismarkIndex/", + gtf : "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Annotation/Genes/genes.gtf", + bed12 : "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Annotation/Genes/genes.bed", + mito_name : "chrM", + macs_gsize : "2.7e9", + blacklist : "${projectDir}/assets/blacklists/hg38-blacklist.bed", + ], + 'CHM13' : [ + fasta : 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"${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/STARIndex/", + bismark : "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/BismarkIndex/", + gtf : "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Annotation/Genes/genes.gtf", + bed12 : "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Annotation/Genes/genes.bed", + readme : "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Annotation/README.txt", + mito_name : "MT", + ], + 'AGPv3' : [ + fasta : "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/WholeGenomeFasta/genome.fa", + bwa : "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/BWAIndex/version0.6.0/", + bowtie2 : "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/Bowtie2Index/", + star : "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/STARIndex/", + bismark : "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/BismarkIndex/", + gtf : "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Annotation/Genes/genes.gtf", + bed12 : "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Annotation/Genes/genes.bed", + mito_name : "Mt", + ], + 'hg38' : [ + fasta : "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/WholeGenomeFasta/genome.fa", + bwa : "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/BWAIndex/version0.6.0/", + bowtie2 : "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/Bowtie2Index/", + star : "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/STARIndex/", + bismark : "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/BismarkIndex/", + gtf : "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Annotation/Genes/genes.gtf", + bed12 : "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Annotation/Genes/genes.bed", + mito_name : "chrM", + macs_gsize : "2.7e9", + blacklist : "${projectDir}/assets/blacklists/hg38-blacklist.bed", + ], + 'hg19' : [ + fasta : "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa", + bwa : "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/BWAIndex/version0.6.0/", + bowtie2 : "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/", + star : "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/STARIndex/", + bismark : "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/BismarkIndex/", + gtf : "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Annotation/Genes/genes.gtf", + bed12 : "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Annotation/Genes/genes.bed", + readme : "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Annotation/README.txt", + mito_name : "chrM", + macs_gsize : "2.7e9", + blacklist : "${projectDir}/assets/blacklists/hg19-blacklist.bed", + ], + 'mm10' : [ + fasta : "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa", + bwa : "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/BWAIndex/version0.6.0/", + bowtie2 : "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/Bowtie2Index/", + star : "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/STARIndex/", + bismark : "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/BismarkIndex/", + gtf : "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Annotation/Genes/genes.gtf", + bed12 : "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Annotation/Genes/genes.bed", + readme : "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Annotation/README.txt", + mito_name : "chrM", + macs_gsize : "1.87e9", + blacklist : "${projectDir}/assets/blacklists/mm10-blacklist.bed", + ], + 'bosTau8' : [ + fasta : "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Sequence/WholeGenomeFasta/genome.fa", + bwa : "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Sequence/BWAIndex/version0.6.0/", + bowtie2 : "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Sequence/Bowtie2Index/", + star : "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Sequence/STARIndex/", + bismark : "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Sequence/BismarkIndex/", + gtf : "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Annotation/Genes/genes.gtf", + bed12 : "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Annotation/Genes/genes.bed", + mito_name : "chrM", + ], + 'ce10' : [ + fasta : "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Sequence/WholeGenomeFasta/genome.fa", + bwa : "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Sequence/BWAIndex/version0.6.0/", + bowtie2 : "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Sequence/Bowtie2Index/", + star : "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Sequence/STARIndex/", + bismark : "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Sequence/BismarkIndex/", + gtf : "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Annotation/Genes/genes.gtf", + bed12 : "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Annotation/Genes/genes.bed", + readme : "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Annotation/README.txt", + mito_name : "chrM", + macs_gsize : "9e7", + ], + 'canFam3' : [ + fasta : "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Sequence/WholeGenomeFasta/genome.fa", + bwa : "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Sequence/BWAIndex/version0.6.0/", + bowtie2 : "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Sequence/Bowtie2Index/", + star : "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Sequence/STARIndex/", + bismark : "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Sequence/BismarkIndex/", + gtf : "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Annotation/Genes/genes.gtf", + bed12 : "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Annotation/Genes/genes.bed", + readme : "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Annotation/README.txt", + mito_name : "chrM", + ], + 'danRer10' : [ + fasta : "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Sequence/WholeGenomeFasta/genome.fa", + bwa : "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Sequence/BWAIndex/version0.6.0/", + bowtie2 : "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Sequence/Bowtie2Index/", + star : "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Sequence/STARIndex/", + bismark : "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Sequence/BismarkIndex/", + gtf : "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Annotation/Genes/genes.gtf", + bed12 : "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Annotation/Genes/genes.bed", + mito_name : "chrM", + macs_gsize : "1.37e9", + ], + 'dm6' : [ + fasta : "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Sequence/WholeGenomeFasta/genome.fa", + bwa : "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Sequence/BWAIndex/version0.6.0/", + bowtie2 : "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Sequence/Bowtie2Index/", + star : "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Sequence/STARIndex/", + bismark : "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Sequence/BismarkIndex/", + gtf : "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Annotation/Genes/genes.gtf", + bed12 : "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Annotation/Genes/genes.bed", + mito_name : "chrM", + macs_gsize : "1.2e8", + ], + 'equCab2' : [ + fasta : "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Sequence/WholeGenomeFasta/genome.fa", + bwa : "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Sequence/BWAIndex/version0.6.0/", + bowtie2 : "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Sequence/Bowtie2Index/", + star : "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Sequence/STARIndex/", + bismark : "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Sequence/BismarkIndex/", + gtf : "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Annotation/Genes/genes.gtf", + bed12 : "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Annotation/Genes/genes.bed", + readme : "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Annotation/README.txt", + mito_name : "chrM", + ], + 'galGal4' : [ + fasta : "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Sequence/WholeGenomeFasta/genome.fa", + bwa : "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Sequence/BWAIndex/version0.6.0/", + bowtie2 : "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Sequence/Bowtie2Index/", + star : "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Sequence/STARIndex/", + bismark : "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Sequence/BismarkIndex/", + gtf : "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Annotation/Genes/genes.gtf", + bed12 : "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Annotation/Genes/genes.bed", + readme : "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Annotation/README.txt", + mito_name : "chrM", + ], + 'panTro4' : [ + fasta : "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Sequence/WholeGenomeFasta/genome.fa", + bwa : "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Sequence/BWAIndex/version0.6.0/", + bowtie2 : "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Sequence/Bowtie2Index/", + star : "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Sequence/STARIndex/", + bismark : "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Sequence/BismarkIndex/", + gtf : "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Annotation/Genes/genes.gtf", + bed12 : "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Annotation/Genes/genes.bed", + readme : "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Annotation/README.txt", + mito_name : "chrM", + ], + 'rn6' : [ + fasta : "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Sequence/WholeGenomeFasta/genome.fa", + bwa : "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Sequence/BWAIndex/version0.6.0/", + bowtie2 : "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Sequence/Bowtie2Index/", + star : "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Sequence/STARIndex/", + bismark : "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Sequence/BismarkIndex/", + gtf : "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Annotation/Genes/genes.gtf", + bed12 : "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Annotation/Genes/genes.bed", + mito_name : "chrM", + ], + 'sacCer3' : [ + fasta : "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/WholeGenomeFasta/genome.fa", + bwa : "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/BWAIndex/version0.6.0/", + bowtie2 : "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/Bowtie2Index/", + star : "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/STARIndex/", + bismark : "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/BismarkIndex/", + readme : "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Annotation/README.txt", + mito_name : "chrM", + macs_gsize : "1.2e7", + ], + 'susScr3' : [ + fasta : "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Sequence/WholeGenomeFasta/genome.fa", + bwa : "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Sequence/BWAIndex/version0.6.0/", + bowtie2 : "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Sequence/Bowtie2Index/", + star : "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Sequence/STARIndex/", + bismark : "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Sequence/BismarkIndex/", + gtf : "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Annotation/Genes/genes.gtf", + bed12 : "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Annotation/Genes/genes.bed", + readme : "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Annotation/README.txt", + mito_name : "chrM", + ], +] diff --git a/conf/modules.config b/conf/modules.config index f0b0d55a..c50e0b7e 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -22,8 +22,7 @@ process { ext.args = { params.multiqc_title ? "--title \"$params.multiqc_title\"" : '' } publishDir = [ path: { "${params.outdir}/multiqc" }, - mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } + mode: params.publish_dir_mode ] } diff --git a/conf/test.config b/conf/test.config index 16c15c34..117abf0c 100644 --- a/conf/test.config +++ b/conf/test.config @@ -5,7 +5,7 @@ Defines input files and everything required to run a fast and simple pipeline test. Use as follows: - nextflow run IntGenomicsLab/lr_somatic -profile test, --outdir + nextflow run IntGenomicsLab/lrsomatic -profile test, --outdir ---------------------------------------------------------------------------------------- */ diff --git a/conf/test_full.config b/conf/test_full.config index 67045bb5..bc82ecba 100644 --- a/conf/test_full.config +++ b/conf/test_full.config @@ -5,7 +5,7 @@ Defines input files and everything required to run a full size pipeline test. Use as follows: - nextflow run IntGenomicsLab/lr_somatic -profile test_full, --outdir + nextflow run IntGenomicsLab/lrsomatic -profile test_full, --outdir ---------------------------------------------------------------------------------------- */ diff --git a/docs/CONTRIBUTING.md b/docs/CONTRIBUTING.md index 468ff202..8d7bdfe7 100644 --- a/docs/CONTRIBUTING.md +++ b/docs/CONTRIBUTING.md @@ -3,15 +3,15 @@ title: Contributing markdownPlugin: checklist --- -# `IntGenomicsLab/lr_somatic`: Contributing guidelines +# `IntGenomicsLab/lrsomatic`: Contributing guidelines Hi there! -Thanks for taking an interest in improving IntGenomicsLab/lr_somatic. +Thanks for taking an interest in improving IntGenomicsLab/lrsomatic. -This page describes the recommended nf-core way to contribute to both IntGenomicsLab/lr_somatic and nf-core pipelines in general, including: +This page describes the recommended nf-core way to contribute to both IntGenomicsLab/lrsomatic and nf-core pipelines in general, including: - [General contribution guidelines](#general-contribution-guidelines): common procedures or guides across all nf-core pipelines. -- [Pipeline-specific contribution guidelines](#pipeline-specific-contribution-guidelines): procedures or guides specific to the development conventions of IntGenomicsLab/lr_somatic. +- [Pipeline-specific contribution guidelines](#pipeline-specific-contribution-guidelines): procedures or guides specific to the development conventions of IntGenomicsLab/lrsomatic. ## General contribution guidelines @@ -20,8 +20,8 @@ This page describes the recommended nf-core way to contribute to both IntGenomic To contribute code to any nf-core pipeline: - [ ] Ensure you have Nextflow, nf-core tools, and nf-test installed. See the [nf-core/tools repository](https://github.com/nf-core/tools) for instructions. -- [ ] Check whether a GitHub [issue](https://github.com/IntGenomicsLab/lr_somatic/issues) about your idea already exists. If an issue does not exist, create one so that others are aware you are working on it. -- [ ] [Fork](https://help.github.com/en/github/getting-started-with-github/fork-a-repo) the [IntGenomicsLab/lr_somatic repository](https://github.com/IntGenomicsLab/lr_somatic) to your GitHub account. +- [ ] Check whether a GitHub [issue](https://github.com/IntGenomicsLab/lrsomatic/issues) about your idea already exists. If an issue does not exist, create one so that others are aware you are working on it. +- [ ] [Fork](https://help.github.com/en/github/getting-started-with-github/fork-a-repo) the [IntGenomicsLab/lrsomatic repository](https://github.com/IntGenomicsLab/lrsomatic) to your GitHub account. - [ ] Create a branch on your forked repository and make your changes following [pipeline conventions](#pipeline-contribution-conventions) (if applicable). - [ ] To fix major bugs, name your branch `patch` and follow the [patch release](#patch-release) process. - [ ] Update relevant documentation within the `docs/` folder, use nf-core/tools to update `nextflow_schema.json`, and update `CITATIONS.md`. @@ -33,13 +33,13 @@ If you are not used to this workflow with Git, see the [GitHub documentation](ht ### GitHub Codespaces -You can contribute to IntGenomicsLab/lr_somatic without installing a local development environment on your machine by using [GitHub Codespaces](https://github.com/codespaces). +You can contribute to IntGenomicsLab/lrsomatic without installing a local development environment on your machine by using [GitHub Codespaces](https://github.com/codespaces). [GitHub Codespaces](https://github.com/codespaces) is an online developer environment that runs in your browser, complete with VS Code and a terminal. Most nf-core repositories include a devcontainer configuration, which creates a GitHub Codespaces environment specifically for Nextflow development. The environment includes pre-installed nf-core tools, Nextflow, and a few other helpful utilities via a Docker container. -To get started, open the repository in [Codespaces](https://github.com/IntGenomicsLab/lr_somatic/codespaces). +To get started, open the repository in [Codespaces](https://github.com/IntGenomicsLab/lrsomatic/codespaces). ### Testing @@ -92,7 +92,7 @@ These tests are run with the latest available version of Nextflow and the minimu ### Pipeline contribution conventions -nf-core semi-standardises how you write code and other contributions to make the IntGenomicsLab/lr_somatic code and processing logic more understandable for new contributors and to ensure quality. +nf-core semi-standardises how you write code and other contributions to make the IntGenomicsLab/lrsomatic code and processing logic more understandable for new contributors and to ensure quality. #### Add a new pipeline step @@ -108,7 +108,7 @@ Please also refer to the [pipeline-specific contribution guidelines](#pipeline-s - [ ] Perform local tests to validate that the new code works as expected. - [ ] If applicable, add a new test in the `tests` directory. - [ ] Update `usage.md`, `output.md`, and `citation.md` as appropriate. -- [ ] [Lint](lint) the code with nf-core/tools. +- [ ] [Lint](#lint-tests) the code with nf-core/tools. - [ ] Update any diagrams or pipeline images as necessary. - [ ] Update MultiQC config `assets/multiqc_config.yml` so relevant suffixes, file name cleanup, and module plots are in the appropriate order. - [ ] If applicable, create a [MultiQC](https://seqera.io/multiqc/) module. @@ -146,7 +146,7 @@ Specify these with generic `withLabel:` selectors, so they can be shared across nf-core provides a set of standard labels that you should follow where possible, as seen in the [nf-core pipeline template](https://github.com/nf-core/tools/blob/main/nf_core/pipeline-template/conf/base.config). These labels define resource defaults for single-core processes, modules that require a GPU, and different levels of multi-core configurations with increasing memory requirements. -Values assigned within these labels can be dynamically passed to a tool using the the `${task.cpus}` and `${task.memory}` Nextflow variables in the `script:` block of a module (see an example in the [modules repository](https://github.com/nf-core/modules/blob/bd1b6a40f55933d94b8c9ca94ec8c1ea0eaf4b82/modules/nf-core/samtools/bam2fq/main.nf#L30)). +Values assigned within these labels can be dynamically passed to a tool using the `${task.cpus}` and `${task.memory}` Nextflow variables in the `script:` block of a module (see an example in the [modules repository](https://github.com/nf-core/modules/blob/bd1b6a40f55933d94b8c9ca94ec8c1ea0eaf4b82/modules/nf-core/samtools/bam2fq/main.nf#L30)). #### Nextflow version bumping diff --git a/docs/README.md b/docs/README.md index 4d1ead62..14889bd3 100644 --- a/docs/README.md +++ b/docs/README.md @@ -1,6 +1,6 @@ -# IntGenomicsLab/lr_somatic: Documentation +# IntGenomicsLab/lrsomatic: Documentation -The IntGenomicsLab/lr_somatic documentation is split into the following pages: +The IntGenomicsLab/lrsomatic documentation is split into the following pages: - [Usage](usage.md) - An overview of how the pipeline works, how to run it and a description of all of the different command-line flags. diff --git a/docs/output.md b/docs/output.md index ed388b30..c3186da4 100644 --- a/docs/output.md +++ b/docs/output.md @@ -1,4 +1,4 @@ -# IntGenomicsLab/lr_somatic: Output +# IntGenomicsLab/lrsomatic: Output ## Introduction @@ -44,4 +44,4 @@ Results generated by MultiQC collate pipeline QC from supported tools e.g. FastQ -[Nextflow](https://www.nextflow.io/docs/latest/tracing.html) provides excellent functionality for generating various reports relevant to the running and execution of the pipeline. This will allow you to troubleshoot errors with the running of the pipeline, and also provide you with other information such as launch commands, run times and resource usage. +[Nextflow](https://docs.seqera.io/platform-cloud/reports/overview) provides excellent functionality for generating various reports relevant to the running and execution of the pipeline. This will allow you to troubleshoot errors with the running of the pipeline, and also provide you with other information such as launch commands, run times and resource usage. diff --git a/docs/usage.md b/docs/usage.md index 1b9ff1bc..ee9becc6 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -1,4 +1,4 @@ -# IntGenomicsLab/lr_somatic: Usage +# IntGenomicsLab/lrsomatic: Usage > _Documentation of pipeline parameters is generated automatically from the pipeline schema and can no longer be found in markdown files._ @@ -55,7 +55,7 @@ An [example samplesheet](../assets/samplesheet.csv) has been provided with the p The typical command for running the pipeline is as follows: ```bash -nextflow run IntGenomicsLab/lr_somatic --input ./samplesheet.csv --outdir ./results --genome GRCh37 -profile docker +nextflow run IntGenomicsLab/lrsomatic --input ./samplesheet.csv --outdir ./results --genome GRCh37 -profile docker ``` This will launch the pipeline with the `docker` configuration profile. See below for more information about profiles. @@ -79,7 +79,7 @@ Pipeline settings can be provided in a `yaml` or `json` file via `-params-file < The above pipeline run specified with a params file in yaml format: ```bash -nextflow run IntGenomicsLab/lr_somatic -profile docker -params-file params.yaml +nextflow run IntGenomicsLab/lrsomatic -profile docker -params-file params.yaml ``` with: @@ -98,14 +98,14 @@ You can also generate such `YAML`/`JSON` files via [nf-core/launch](https://nf-c When you run the above command, Nextflow automatically pulls the pipeline code from GitHub and stores it as a cached version. When running the pipeline after this, it will always use the cached version if available - even if the pipeline has been updated since. To make sure that you're running the latest version of the pipeline, make sure that you regularly update the cached version of the pipeline: ```bash -nextflow pull IntGenomicsLab/lr_somatic +nextflow pull IntGenomicsLab/lrsomatic ``` ### Reproducibility It is a good idea to specify the pipeline version when running the pipeline on your data. This ensures that a specific version of the pipeline code and software are used when you run your pipeline. If you keep using the same tag, you'll be running the same version of the pipeline, even if there have been changes to the code since. -First, go to the [IntGenomicsLab/lr_somatic releases page](https://github.com/IntGenomicsLab/lr_somatic/releases) and find the latest pipeline version - numeric only (eg. `1.3.1`). Then specify this when running the pipeline with `-r` (one hyphen) - eg. `-r 1.3.1`. Of course, you can switch to another version by changing the number after the `-r` flag. +First, go to the [IntGenomicsLab/lrsomatic releases page](https://github.com/IntGenomicsLab/lrsomatic/releases) and find the latest pipeline version - numeric only (eg. `1.3.1`). Then specify this when running the pipeline with `-r` (one hyphen) - eg. `-r 1.3.1`. Of course, you can switch to another version by changing the number after the `-r` flag. This version number will be logged in reports when you run the pipeline, so that you'll know what you used when you look back in the future. For example, at the bottom of the MultiQC reports. @@ -151,7 +151,7 @@ If `-profile` is not specified, the pipeline will run locally and expect all sof - `apptainer` - A generic configuration profile to be used with [Apptainer](https://apptainer.org/) - `wave` - - A generic configuration profile to enable [Wave](https://seqera.io/wave/) containers. Use together with one of the above (requires Nextflow ` 24.03.0-edge` or later). + - A generic configuration profile to enable [Wave](https://seqera.io/wave/) containers. Use together with one of the above (requires Nextflow `24.03.0-edge` or later). - `conda` - A generic configuration profile to be used with [Conda](https://conda.io/docs/). Please only use Conda as a last resort i.e. when it's not possible to run the pipeline with Docker, Singularity, Podman, Shifter, Charliecloud, or Apptainer. diff --git a/main.nf b/main.nf index a32609b1..d1586fb0 100644 --- a/main.nf +++ b/main.nf @@ -1,9 +1,9 @@ #!/usr/bin/env nextflow /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - IntGenomicsLab/lr_somatic + IntGenomicsLab/lrsomatic ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - Github : https://github.com/IntGenomicsLab/lr_somatic + Github : https://github.com/IntGenomicsLab/lrsomatic ---------------------------------------------------------------------------------------- */ @@ -13,10 +13,10 @@ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ -include { LR_SOMATIC } from './workflows/lr_somatic' -include { PIPELINE_INITIALISATION } from './subworkflows/local/utils_nfcore_lr_somatic_pipeline' -include { PIPELINE_COMPLETION } from './subworkflows/local/utils_nfcore_lr_somatic_pipeline' -include { getGenomeAttribute } from './subworkflows/local/utils_nfcore_lr_somatic_pipeline' +include { LRSOMATIC } from './workflows/lrsomatic' +include { PIPELINE_INITIALISATION } from './subworkflows/local/utils_nfcore_lrsomatic_pipeline' +include { PIPELINE_COMPLETION } from './subworkflows/local/utils_nfcore_lrsomatic_pipeline' +include { getGenomeAttribute } from './subworkflows/local/utils_nfcore_lrsomatic_pipeline' /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -38,7 +38,7 @@ params.fasta = getGenomeAttribute('fasta') // // WORKFLOW: Run main analysis pipeline depending on type of input // -workflow INTGENOMICSLAB_LR_SOMATIC { +workflow INTGENOMICSLAB_LRSOMATIC { take: samplesheet // channel: samplesheet read in from --input @@ -48,7 +48,7 @@ workflow INTGENOMICSLAB_LR_SOMATIC { // // WORKFLOW: Run pipeline // - LR_SOMATIC ( + LRSOMATIC ( samplesheet, params.multiqc_config, params.multiqc_logo, @@ -56,7 +56,7 @@ workflow INTGENOMICSLAB_LR_SOMATIC { params.outdir, ) emit: - multiqc_report = LR_SOMATIC.out.multiqc_report // channel: /path/to/multiqc_report.html + multiqc_report = LRSOMATIC.out.multiqc_report // channel: /path/to/multiqc_report.html } /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -85,7 +85,7 @@ workflow { // // WORKFLOW: Run main workflow // - INTGENOMICSLAB_LR_SOMATIC ( + INTGENOMICSLAB_LRSOMATIC ( PIPELINE_INITIALISATION.out.samplesheet ) // @@ -97,7 +97,7 @@ workflow { params.plaintext_email, params.outdir, params.monochrome_logs, - INTGENOMICSLAB_LR_SOMATIC.out.multiqc_report + INTGENOMICSLAB_LRSOMATIC.out.multiqc_report ) } diff --git a/modules.json b/modules.json index ca14915c..94325c4f 100644 --- a/modules.json +++ b/modules.json @@ -1,13 +1,13 @@ { - "name": "IntGenomicsLab/lr_somatic", - "homePage": "https://github.com/IntGenomicsLab/lr_somatic", + "name": "IntGenomicsLab/lrsomatic", + "homePage": "https://github.com/IntGenomicsLab/lrsomatic", "repos": { "https://github.com/nf-core/modules.git": { "modules": { "nf-core": { "multiqc": { "branch": "master", - "git_sha": "008f9d3e61209bf995edac3ba531f54e269e1215", + "git_sha": "98403d15b0e50edae1f3fec5eae5e24982f1fade", "installed_by": ["modules"] } } @@ -16,7 +16,7 @@ "nf-core": { "utils_nextflow_pipeline": { "branch": "master", - "git_sha": "05954dab2ff481bcb999f24455da29a5828af08d", + "git_sha": "c2b22d85f30a706a3073387f30380704fcae013b", "installed_by": ["subworkflows"] }, "utils_nfcore_pipeline": { @@ -26,7 +26,7 @@ }, "utils_nfschema_plugin": { "branch": "master", - "git_sha": "fdc08b8b1ae74f56686ce21f7ea11ad11990ce57", + "git_sha": "a7b27fd25bfa8dcc07d299e88bd790585901a436", "installed_by": ["subworkflows"] } } diff --git a/modules/nf-core/multiqc/.conda-lock/linux_amd64-bd-c17fb751507e9dfc_1.txt b/modules/nf-core/multiqc/.conda-lock/linux_amd64-bd-c17fb751507e9dfc_1.txt new 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bioconda::multiqc=1.35 diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf index e80e8cd8..c4bc715e 100644 --- a/modules/nf-core/multiqc/main.nf +++ b/modules/nf-core/multiqc/main.nf @@ -4,8 +4,8 @@ process MULTIQC { conda "${moduleDir}/environment.yml" container "${workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container - ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/1b/1bef8af6be88c5733461959c46ac8ef73d18f65277f62a1695d0e1633054f9c2/data' - : 'community.wave.seqera.io/library/multiqc:1.34--db7c73dae76bc9e6'}" + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/c8/c8e346f4f6080eadf1253505e6ff09ef004454fc18e8d672006fd7b222cc412e/data' + : 'community.wave.seqera.io/library/multiqc:1.35--c17fb751507e9dfc'}" input: tuple val(meta), path(multiqc_files, stageAs: "?/*"), path(multiqc_config, stageAs: "?/*"), path(multiqc_logo), path(replace_names), path(sample_names) diff --git a/modules/nf-core/multiqc/meta.yml b/modules/nf-core/multiqc/meta.yml index 2facc627..27ce18d8 100644 --- a/modules/nf-core/multiqc/meta.yml +++ b/modules/nf-core/multiqc/meta.yml @@ -110,24 +110,24 @@ maintainers: containers: conda: linux/amd64: - lock_file: modules/nf-core/multiqc/.conda-lock/linux_amd64-bd-db7c73dae76bc9e6_1.txt + lock_file: modules/nf-core/multiqc/.conda-lock/linux_amd64-bd-c17fb751507e9dfc_1.txt linux/arm64: - lock_file: modules/nf-core/multiqc/.conda-lock/linux_arm64-bd-d167b8012595a136_1.txt + lock_file: modules/nf-core/multiqc/.conda-lock/linux_arm64-bd-5c84a5000a226ab5_1.txt docker: linux/amd64: - name: community.wave.seqera.io/library/multiqc:1.34--db7c73dae76bc9e6 - build_id: bd-db7c73dae76bc9e6_1 - scan_id: sc-66fc7138dbf1cf48_1 + name: community.wave.seqera.io/library/multiqc:1.35--c17fb751507e9dfc + build_id: bd-c17fb751507e9dfc_1 + scan_id: sc-3b1b3932f9846892_1 linux/arm64: - name: community.wave.seqera.io/library/multiqc:1.34--d167b8012595a136 - build_id: bd-d167b8012595a136_1 - scan_id: sc-ac701dfa631a2af9_1 + name: community.wave.seqera.io/library/multiqc:1.35--5c84a5000a226ab5 + build_id: bd-5c84a5000a226ab5_1 + scan_id: sc-0d39df41e9737bbd_1 singularity: linux/amd64: - name: oras://community.wave.seqera.io/library/multiqc:1.34--4fc8657c816047c0 - build_id: bd-4fc8657c816047c0_1 - https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/1b/1bef8af6be88c5733461959c46ac8ef73d18f65277f62a1695d0e1633054f9c2/data + name: oras://community.wave.seqera.io/library/multiqc:1.35--c680f2aea25ccec2 + build_id: bd-c680f2aea25ccec2_1 + https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/c8/c8e346f4f6080eadf1253505e6ff09ef004454fc18e8d672006fd7b222cc412e/data linux/arm64: - name: oras://community.wave.seqera.io/library/multiqc:1.34--7fbd82d945c06726 - build_id: bd-7fbd82d945c06726_1 - https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/9a/9a1fec9662a152683e6fcae440d0ce20920b3b89dc62d1e3a52e73f92eba0969/data + name: oras://community.wave.seqera.io/library/multiqc:1.35--c0468833d65b2f81 + build_id: bd-c0468833d65b2f81_1 + https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/e4/e48aa28aebc881254a499b24c3e1ce77b8df1b85a5432699ed6f72eb17ac7fb5/data diff --git a/modules/nf-core/multiqc/tests/main.nf.test.snap b/modules/nf-core/multiqc/tests/main.nf.test.snap index 7c2f370f..44899216 100644 --- a/modules/nf-core/multiqc/tests/main.nf.test.snap +++ b/modules/nf-core/multiqc/tests/main.nf.test.snap @@ -81,7 +81,7 @@ [ "MULTIQC", "multiqc", - "1.34" + "1.35" ] ] } @@ -175,7 +175,7 @@ [ "MULTIQC", "multiqc", - "1.34" + "1.35" ] ] } @@ -221,7 +221,7 @@ [ "MULTIQC", "multiqc", - "1.34" + "1.35" ] ] } @@ -314,7 +314,7 @@ [ "MULTIQC", "multiqc", - "1.34" + "1.35" ] ] } @@ -408,7 +408,7 @@ [ "MULTIQC", "multiqc", - "1.34" + "1.35" ] ] } diff --git a/nextflow.config b/nextflow.config index 07b1a931..7dea9172 100644 --- a/nextflow.config +++ b/nextflow.config @@ -1,6 +1,6 @@ /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - IntGenomicsLab/lr_somatic Nextflow config file + IntGenomicsLab/lrsomatic Nextflow config file ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Default config options for all compute environments ---------------------------------------------------------------------------------------- @@ -176,13 +176,13 @@ profiles { // 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 IntGenomicsLab/lr_somatic custom profiles from different institutions. +// Load IntGenomicsLab/lrsomatic 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 IntGenomicsLab/lr_somatic custom profiles from different institutions. +// Load IntGenomicsLab/lrsomatic custom profiles from different institutions. // TODO nf-core: Optionally, you can add a pipeline-specific nf-core config at https://github.com/nf-core/configs -// includeConfig params.custom_config_base && (!System.getenv('NXF_OFFLINE') || !params.custom_config_base.startsWith('http')) ? "${params.custom_config_base}/pipeline/lr_somatic.config" : "/dev/null" +// includeConfig params.custom_config_base && (!System.getenv('NXF_OFFLINE') || !params.custom_config_base.startsWith('http')) ? "${params.custom_config_base}/pipeline/lrsomatic.config" : "/dev/null" // 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 @@ -238,11 +238,11 @@ dag { } manifest { - name = 'IntGenomicsLab/lr_somatic' + name = 'IntGenomicsLab/lrsomatic' contributors = [ // TODO nf-core: Update the field with the details of the contributors to your pipeline. New with Nextflow version 24.10.0 [ - name: 'Jonas Demeulemeester', + name: 'Robert Forsyth & Luuk Harbers', affiliation: '', email: '', github: '', @@ -250,12 +250,12 @@ manifest { orcid: '' ], ] - homePage = 'https://github.com/IntGenomicsLab/lr_somatic' + homePage = 'https://github.com/IntGenomicsLab/lrsomatic' description = """Workflow for somatic variant calling of long read data""" mainScript = 'main.nf' defaultBranch = 'main' nextflowVersion = '!>=25.10.4' - version = '1.0.0dev' + version = '1.1.0' doi = '' } diff --git a/nextflow_schema.json b/nextflow_schema.json index 0bd3227b..64df1c2d 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -1,7 +1,7 @@ { "$schema": "https://json-schema.org/draft/2020-12/schema", - "$id": "https://raw.githubusercontent.com/IntGenomicsLab/lr_somatic/main/nextflow_schema.json", - "title": "IntGenomicsLab/lr_somatic pipeline parameters", + "$id": "https://raw.githubusercontent.com/IntGenomicsLab/lrsomatic/main/nextflow_schema.json", + "title": "IntGenomicsLab/lrsomatic pipeline parameters", "description": "Workflow for somatic variant calling of long read data", "type": "object", "$defs": { @@ -74,7 +74,6 @@ }, "igenomes_base": { "type": "string", - "format": "directory-path", "description": "The base path to the igenomes reference files", "fa_icon": "fas fa-ban", "hidden": true, diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json index 1cc3153c..c34b41cd 100644 --- a/ro-crate-metadata.json +++ b/ro-crate-metadata.json @@ -21,9 +21,9 @@ { "@id": "./", "@type": "Dataset", - "creativeWorkStatus": "InProgress", - "datePublished": "2026-04-29T11:16:38+00:00", - "description": "# IntGenomicsLab/lr_somatic\n\n[![Open in GitHub Codespaces](https://img.shields.io/badge/Open_In_GitHub_Codespaces-black?labelColor=grey&logo=github)](https://github.com/codespaces/new/IntGenomicsLab/lr_somatic)\n[![GitHub Actions CI Status](https://github.com/IntGenomicsLab/lr_somatic/actions/workflows/nf-test.yml/badge.svg)](https://github.com/IntGenomicsLab/lr_somatic/actions/workflows/nf-test.yml)\n[![GitHub Actions Linting Status](https://github.com/IntGenomicsLab/lr_somatic/actions/workflows/linting.yml/badge.svg)](https://github.com/IntGenomicsLab/lr_somatic/actions/workflows/linting.yml)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n\n[![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.10.4-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)\n[![nf-core template version](https://img.shields.io/badge/nf--core_template-4.0.1-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/4.0.1)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/IntGenomicsLab/lr_somatic)\n\n## Introduction\n\n**IntGenomicsLab/lr_somatic** is a bioinformatics pipeline that ...\n\n\n\n\n2. Present QC for raw reads ([`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/get_started/environment_setup/overview) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/get_started/run-your-first-pipeline) with `-profile test` before running the workflow on actual data.\n\n\n\nNow, you can run the pipeline using:\n\n\n\n```bash\nnextflow run IntGenomicsLab/lr_somatic \\\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**_; see [docs](https://nf-co.re/docs/running/run-pipelines#using-parameter-files).\n\n## Credits\n\nIntGenomicsLab/lr_somatic was originally written by Jonas Demeulemeester.\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](docs/CONTRIBUTING.md).\n\n## Citations\n\n\n\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 uses 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/main/LICENSE).\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", + "creativeWorkStatus": "Stable", + "datePublished": "2026-08-14T13:33:32+00:00", + "description": "# IntGenomicsLab/lrsomatic\n\n[![Open in GitHub Codespaces](https://img.shields.io/badge/Open_In_GitHub_Codespaces-black?labelColor=grey&logo=github)](https://github.com/codespaces/new/IntGenomicsLab/lrsomatic)\n[![GitHub Actions CI Status](https://github.com/IntGenomicsLab/lrsomatic/actions/workflows/nf-test.yml/badge.svg)](https://github.com/IntGenomicsLab/lrsomatic/actions/workflows/nf-test.yml)\n[![GitHub Actions Linting Status](https://github.com/IntGenomicsLab/lrsomatic/actions/workflows/linting.yml/badge.svg)](https://github.com/IntGenomicsLab/lrsomatic/actions/workflows/linting.yml)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n\n[![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.10.4-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)\n[![nf-core template version](https://img.shields.io/badge/nf--core_template-4.1.0-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/4.1.0)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/IntGenomicsLab/lrsomatic)\n\n## Introduction\n\n**IntGenomicsLab/lrsomatic** is a bioinformatics pipeline that ...\n\n\n\n\n2. Present QC for raw reads ([`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/get_started/environment_setup/overview) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/get_started/run-your-first-pipeline) with `-profile test` before running the workflow on actual data.\n\n\n\nNow, you can run the pipeline using:\n\n\n\n```bash\nnextflow run IntGenomicsLab/lrsomatic \\\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**_; see [docs](https://nf-co.re/docs/running/run-pipelines#using-parameter-files).\n\n## Credits\n\nIntGenomicsLab/lrsomatic was originally written by Robert Forsyth & Luuk Harbers.\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](docs/CONTRIBUTING.md).\n\n## Citations\n\n\n\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 uses 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/main/LICENSE).\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" @@ -86,17 +86,17 @@ "@id": ".prettierignore" } ], - "isBasedOn": "https://github.com/IntGenomicsLab/lr_somatic", + "isBasedOn": "https://github.com/IntGenomicsLab/lrsomatic", "license": "MIT", "mainEntity": { "@id": "main.nf" }, "mentions": [ { - "@id": "#b187d946-a3e5-4ddc-bcb4-229b90fdaa92" + "@id": "#ded8aa2d-e051-4884-94b1-3be4483d2ca4" } ], - "name": "IntGenomicsLab/lr_somatic" + "name": "IntGenomicsLab/lrsomatic" }, { "@id": "ro-crate-metadata.json", @@ -120,13 +120,8 @@ "SoftwareSourceCode", "ComputationalWorkflow" ], - "contributor": [ - { - "@id": "https://orcid.org/0000-0002-2660-2478" - } - ], "dateCreated": "", - "dateModified": "2026-04-29T13:16:38Z", + "dateModified": "2026-08-14T15:33:32Z", "dct:conformsTo": "https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE/", "keywords": [ "nf-core", @@ -136,7 +131,7 @@ "MIT" ], "name": [ - "IntGenomicsLab/lr_somatic" + "IntGenomicsLab/lrsomatic" ], "programmingLanguage": { "@id": "https://w3id.org/workflowhub/workflow-ro-crate#nextflow" @@ -145,11 +140,12 @@ "@id": "https://nf-co.re/" }, "url": [ - "https://github.com/IntGenomicsLab/lr_somatic", - "https://nf-co.re/IntGenomicsLab/lr_somatic/dev/" + "https://github.com/IntGenomicsLab/lrsomatic", + "https://nf-co.re/IntGenomicsLab/lrsomatic//" ], "version": [ - "1.0.0dev" + "", + "1.1.0" ] }, { @@ -165,23 +161,23 @@ "version": "!>=25.10.4" }, { - "@id": "#b187d946-a3e5-4ddc-bcb4-229b90fdaa92", + "@id": "#ded8aa2d-e051-4884-94b1-3be4483d2ca4", "@type": "TestSuite", "instance": [ { - "@id": "#7273b88e-2152-44cd-81ef-604abcc610ae" + "@id": "#0a084c28-c353-4696-acfc-3e7c84fdf983" } ], "mainEntity": { "@id": "main.nf" }, - "name": "Test suite for IntGenomicsLab/lr_somatic" + "name": "Test suite for IntGenomicsLab/lrsomatic" }, { - "@id": "#7273b88e-2152-44cd-81ef-604abcc610ae", + "@id": "#0a084c28-c353-4696-acfc-3e7c84fdf983", "@type": "TestInstance", - "name": "GitHub Actions workflow for testing IntGenomicsLab/lr_somatic", - "resource": "repos/IntGenomicsLab/lr_somatic/actions/workflows/nf-test.yml", + "name": "GitHub Actions workflow for testing IntGenomicsLab/lrsomatic", + "resource": "repos/IntGenomicsLab/lrsomatic/actions/workflows/nf-test.yml", "runsOn": { "@id": "https://w3id.org/ro/terms/test#GithubService" }, @@ -295,11 +291,6 @@ "@type": "Organization", "name": "nf-core", "url": "https://nf-co.re/" - }, - { - "@id": "https://orcid.org/0000-0002-2660-2478", - "@type": "Person", - "name": "Jonas Demeulemeester" } ] } \ No newline at end of file diff --git a/subworkflows/local/utils_nfcore_lr_somatic_pipeline/main.nf b/subworkflows/local/utils_nfcore_lrsomatic_pipeline/main.nf similarity index 99% rename from subworkflows/local/utils_nfcore_lr_somatic_pipeline/main.nf rename to subworkflows/local/utils_nfcore_lrsomatic_pipeline/main.nf index a49dfe4b..87df1bdf 100644 --- a/subworkflows/local/utils_nfcore_lr_somatic_pipeline/main.nf +++ b/subworkflows/local/utils_nfcore_lrsomatic_pipeline/main.nf @@ -1,5 +1,5 @@ // -// Subworkflow with functionality specific to the IntGenomicsLab/lr_somatic pipeline +// Subworkflow with functionality specific to the IntGenomicsLab/lrsomatic pipeline // /* @@ -71,7 +71,8 @@ workflow PIPELINE_INITIALISATION { show_hidden, before_text, after_text, - command + command, + false ) // diff --git a/subworkflows/nf-core/utils_nfschema_plugin/main.nf b/subworkflows/nf-core/utils_nfschema_plugin/main.nf index 1df8b76f..9ff0681f 100644 --- a/subworkflows/nf-core/utils_nfschema_plugin/main.nf +++ b/subworkflows/nf-core/utils_nfschema_plugin/main.nf @@ -22,6 +22,7 @@ workflow UTILS_NFSCHEMA_PLUGIN { 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 + cli_typecast // boolean: whether to perform typecasting of CLI parameters. Set this to `null` to use the default behaviour main: @@ -34,11 +35,11 @@ workflow UTILS_NFSCHEMA_PLUGIN { fullHelp: help_full, ] if(parameters_schema) { - help_options << [parametersSchema: parameters_schema] + help_options << [parameters_schema: parameters_schema] } log.info paramsHelp( help_options, - (params.help instanceof String && params.help != "true") ? params.help : "", + (help instanceof String && help != "true") ? help : "", ) exit 0 } @@ -50,7 +51,7 @@ workflow UTILS_NFSCHEMA_PLUGIN { summary_options = [:] if(parameters_schema) { - summary_options << [parametersSchema: parameters_schema] + summary_options << [parameters_schema: parameters_schema] } log.info before_text log.info paramsSummaryLog(summary_options, input_workflow) @@ -63,7 +64,10 @@ workflow UTILS_NFSCHEMA_PLUGIN { if(validate_params) { validateOptions = [:] if(parameters_schema) { - validateOptions << [parametersSchema: parameters_schema] + validateOptions << [parameters_schema: parameters_schema] + } + if(cli_typecast != null) { + validateOptions << [cast_cli_params: cli_typecast] } validateParameters(validateOptions) } diff --git a/subworkflows/nf-core/utils_nfschema_plugin/meta.yml b/subworkflows/nf-core/utils_nfschema_plugin/meta.yml index f7d9f028..1d8c75a9 100644 --- a/subworkflows/nf-core/utils_nfschema_plugin/meta.yml +++ b/subworkflows/nf-core/utils_nfschema_plugin/meta.yml @@ -25,6 +25,30 @@ input: option. When this input is empty it will automatically use the configured schema or "${projectDir}/nextflow_schema.json" as default. The schema should not be given in this way for meta pipelines. + - help: + type: boolean, string + description: | + Show the help message and exit. When a parameter name is given, show the help message for that parameter instead of the general help message. + - help_full: + type: boolean + description: Show the full help message and exit. + - show_hidden: + type: boolean + description: Show hidden parameters in the help message. + - before_text: + type: string + description: Text to show before the parameters summary and help message. + - after_text: + type: string + description: Text to show after the parameters summary and help message. + - command: + type: string + description: An example command to run the pipeline, to show in the help message and the summary. + - cli_typecast: + type: boolean + description: | + Whether to apply typecasting to the parameters given via the CLI before validation. + Set this to `null` to use the default behavior. output: - dummy_emit: type: boolean 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 c977917a..1fd1eac1 100644 --- a/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test +++ b/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test @@ -31,6 +31,7 @@ nextflow_workflow { input[6] = "" input[7] = "" input[8] = "" + input[9] = null """ } } @@ -63,6 +64,7 @@ nextflow_workflow { input[6] = "" input[7] = "" input[8] = "" + input[9] = null """ } } @@ -95,6 +97,7 @@ nextflow_workflow { input[6] = "" input[7] = "" input[8] = "" + input[9] = null """ } } @@ -127,6 +130,7 @@ nextflow_workflow { input[6] = "" input[7] = "" input[8] = "" + input[9] = null """ } } @@ -160,6 +164,7 @@ nextflow_workflow { input[6] = "Before" input[7] = "After" input[8] = "nextflow run test/test" + input[9] = null """ } } diff --git a/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config b/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config index f6537cc3..fd71cb8f 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@2.6.1" + id "nf-schema@2.7.2" } validation { diff --git a/tests/default.nf.test b/tests/default.nf.test index bfedd460..bdcaf592 100644 --- a/tests/default.nf.test +++ b/tests/default.nf.test @@ -21,7 +21,7 @@ nextflow_pipeline { assertAll( { assert snapshot( // pipeline versions.yml file for multiqc from which Nextflow version is removed because we test pipelines on multiple Nextflow versions - removeNextflowVersion("$outputDir/pipeline_info/lr_somatic_software_mqc_versions.yml"), + removeNextflowVersion("$outputDir/pipeline_info/lrsomatic_software_mqc_versions.yml"), // All stable path name, with a relative path stable_path, // All files with stable contents diff --git a/tests/nextflow.config b/tests/nextflow.config index 97db1b82..910d0466 100644 --- a/tests/nextflow.config +++ b/tests/nextflow.config @@ -8,7 +8,8 @@ // Or any resources requirements 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/lr_somatic/' + pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/lrsomatic/' } -aws.client.anonymous = true // fixes S3 access issues on self-hosted runners +// Fixes S3 access issues on self-hosted runners +aws.client.anonymous = true diff --git a/workflows/lr_somatic.nf b/workflows/lrsomatic.nf similarity index 95% rename from workflows/lr_somatic.nf rename to workflows/lrsomatic.nf index 73367881..0b157aac 100644 --- a/workflows/lr_somatic.nf +++ b/workflows/lrsomatic.nf @@ -7,7 +7,7 @@ include { MULTIQC } from '../modules/nf-core/multiqc/main' include { paramsSummaryMap } from 'plugin/nf-schema' include { paramsSummaryMultiqc } from '../subworkflows/nf-core/utils_nfcore_pipeline' include { softwareVersionsToYAML } from '../subworkflows/nf-core/utils_nfcore_pipeline' -include { methodsDescriptionText } from '../subworkflows/local/utils_nfcore_lr_somatic_pipeline' +include { methodsDescriptionText } from '../subworkflows/local/utils_nfcore_lrsomatic_pipeline' /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -15,7 +15,7 @@ include { methodsDescriptionText } from '../subworkflows/local/utils_nfcore_lr_s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ -workflow LR_SOMATIC { +workflow LRSOMATIC { take: ch_samplesheet // channel: samplesheet read in from --input @@ -53,7 +53,7 @@ workflow LR_SOMATIC { .mix(topic_versions_string) .collectFile( storeDir: "${outdir}/pipeline_info", - name: 'lr_somatic_software_' + 'mqc_' + 'versions.yml', + name: 'lrsomatic_software_' + 'mqc_' + 'versions.yml', sort: true, newLine: true ) @@ -73,7 +73,7 @@ workflow LR_SOMATIC { MULTIQC( ch_multiqc_files.flatten().collect().map { files -> [ - [id: 'lr_somatic'], + [id: 'lrsomatic'], files, multiqc_config ? file(multiqc_config, checkIfExists: true) From 58dddeaf0a6656c5d546fc31749f5d28def8138a Mon Sep 17 00:00:00 2001 From: ljwharbers Date: Fri, 14 Aug 2026 15:53:48 +0200 Subject: [PATCH 2/6] fix: add missing trailing newline to .gitignore The 4.1.0 template's end-of-file-fixer pre-commit hook flags this pre-existing issue, which would fail the linting workflow. Co-Authored-By: Claude Opus 5 --- .gitignore | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.gitignore b/.gitignore index fb6eca4c..00ba0481 100644 --- a/.gitignore +++ b/.gitignore @@ -11,4 +11,4 @@ null/ .nf-test/ .nf-test.log CLAUDE.local.md -.claude/ \ No newline at end of file +.claude/ From 204c21aa22a0e41b792cc81197cdda3db395cb78 Mon Sep 17 00:00:00 2001 From: ljwharbers Date: Fri, 14 Aug 2026 16:03:41 +0200 Subject: [PATCH 3/6] docs: add CHANGELOG entry for the 4.1.0 template sync Co-Authored-By: Claude Opus 5 --- CHANGELOG.md | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index c563127c..a9c4138a 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -5,6 +5,12 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ## v1.2.0dev +### `Changed` + +- Updated to the nf-core template for [nf-core/tools 4.1.0](https://github.com/nf-core/tools/releases/tag/4.1.0). Adds the `check-added-large-files`, `check-merge-conflict` and `block-pipeline-outdir` pre-commit hooks, a `process_low_memory` resource label, and a split-out `pr-comment.yml` workflow. `conf/igenomes.config` was converted to the template's strict-syntax `params.genomes` map literal, and the MultiQC module was bumped to 1.35. +- Raised the minimum Nextflow version to `25.10.4`, following the template, and bumped the nf-test CI matrix to match. +- Filled in the `manifest.contributors` `contribution` fields: @ljwharbers and @robert-a-forsyth as author and maintainer, all other contributors as author. Previously empty, which left the RO-Crate metadata without any authors. + ### `Fixed` - [#182](https://github.com/IntGenomicsLab/lrsomatic/pull/182) - Added `--vcf` to the default `vep_args` so VEP writes VCF output rather than its default tab-delimited format (@AmberVerhasselt). From 18060ef7ce74bb517afd6dde24372a9398d4f112 Mon Sep 17 00:00:00 2001 From: ljwharbers Date: Tue, 18 Aug 2026 14:53:50 +0200 Subject: [PATCH 4/6] docs: add Amber Verhasselt as contributor, expand Luuk Harbers' affiliation Adds @AmberVerhasselt to `manifest.contributors` with contribution type `contributor`, placed after @robert-a-forsyth, and to the README credits. Luuk Harbers' affiliation is expanded to the same three-part string the other core contributors carry. `ro-crate-metadata.json` is updated by hand to match: a new Person entity for Amber, a new `contributor` array on the workflow entity, the updated affiliation, and the same credits sentence in the embedded README description (kept byte-identical so `rocrate_readme_sync` does not rewrite the file and escape the non-ASCII names). Co-Authored-By: Claude Opus 5 --- CHANGELOG.md | 1 + README.md | 2 +- nextflow.config | 10 +++++++++- ro-crate-metadata.json | 17 +++++++++++++++-- 4 files changed, 26 insertions(+), 4 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index a9c4138a..ce04fb44 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -10,6 +10,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - Updated to the nf-core template for [nf-core/tools 4.1.0](https://github.com/nf-core/tools/releases/tag/4.1.0). Adds the `check-added-large-files`, `check-merge-conflict` and `block-pipeline-outdir` pre-commit hooks, a `process_low_memory` resource label, and a split-out `pr-comment.yml` workflow. `conf/igenomes.config` was converted to the template's strict-syntax `params.genomes` map literal, and the MultiQC module was bumped to 1.35. - Raised the minimum Nextflow version to `25.10.4`, following the template, and bumped the nf-test CI matrix to match. - Filled in the `manifest.contributors` `contribution` fields: @ljwharbers and @robert-a-forsyth as author and maintainer, all other contributors as author. Previously empty, which left the RO-Crate metadata without any authors. +- Added @AmberVerhasselt to `manifest.contributors` as a contributor and to the README credits, and expanded @ljwharbers' affiliation to match the other core contributors. RO-Crate metadata updated to match. ### `Fixed` diff --git a/README.md b/README.md index 4288d7bd..ac7699c5 100644 --- a/README.md +++ b/README.md @@ -100,7 +100,7 @@ More detail is given in our [usage documentation](/docs/usage.md) ## Credits -IntGenomicsLab/lr_somatic was originally written by Luuk Harbers, Robert Forsyth, Alexandra Pančíková, Marios Eftychiou, Ruben Cools, Laurens Lambrechts, and Jonas Demeulemeester. +IntGenomicsLab/lr_somatic was originally written by Luuk Harbers, Robert Forsyth, Amber Verhasselt, Alexandra Pančíková, Marios Eftychiou, Ruben Cools, Laurens Lambrechts, and Jonas Demeulemeester. ## Pipeline output diff --git a/nextflow.config b/nextflow.config index dddb6583..b253829e 100644 --- a/nextflow.config +++ b/nextflow.config @@ -313,7 +313,7 @@ manifest { // TODO nf-core: Update the field with the details of the contributors to your pipeline. New with Nextflow version 24.10.0 [ name: 'Luuk Harbers', - affiliation: 'VIB Center for Cancer Biology, VIB, Leuven, Belgium', + affiliation: 'VIB Center for Cancer Biology, VIB, Leuven, Belgium; Laboratory of Integrative Cancer Genomics, Department of Oncology, KU Leuven, Leuven, Belgium; VIB Center for AI and Computational Biology, VIB, Leuven, Belgium', email: 'luuk.harbers@kuleuven.be', github: 'https://github.com/ljwharbers', contribution: ['author', 'maintainer'], // List of contribution types ('author', 'maintainer' or 'contributor') @@ -327,6 +327,14 @@ manifest { contribution: ['author', 'maintainer'], // List of contribution types ('author', 'maintainer' or 'contributor') orcid: 'https://orcid.org/0000-0002-6202-8477' ], + [ + name: 'Amber Verhasselt', + affiliation: 'Laboratory for Genetics of Malignant Disorders, Department of Human Genetics, KU Leuven, Leuven, Belgium', + email: 'amber.verhasselt@kuleuven.be', + github: 'https://github.com/AmberVerhasselt', + contribution: ['contributor'], // List of contribution types ('author', 'maintainer' or 'contributor') + orcid: 'https://orcid.org/0009-0000-4447-9795' + ], [ name: 'Alexandra Pančíková', affiliation: 'VIB Center for Cancer Biology, VIB, Leuven, Belgium; Laboratory of Integrative Cancer Genomics, Department of Oncology, KU Leuven, Leuven, Belgium; VIB Center for AI and Computational Biology, VIB, Leuven, Belgium; Laboratory for Computational Biology, Department of Human Genetics, KU Leuven, Leuven, Belgium; VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium', diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json index 2bfae58f..590f4219 100644 --- a/ro-crate-metadata.json +++ b/ro-crate-metadata.json @@ -23,7 +23,7 @@ "@type": "Dataset", "creativeWorkStatus": "Stable", "datePublished": "2026-08-14T13:41:35+00:00", - "description": "# IntGenomicsLab/lrsomatic\n\n[![Open in GitHub Codespaces](https://img.shields.io/badge/Open_In_GitHub_Codespaces-black?labelColor=grey&logo=github)](https://github.com/codespaces/new/IntGenomicsLab/lrsomatic)\n[![GitHub Actions CI Status](https://github.com/IntGenomicsLab/lrsomatic/actions/workflows/nf-test.yml/badge.svg)](https://github.com/IntGenomicsLab/lrsomatic/actions/workflows/nf-test.yml)\n[![GitHub Actions Linting Status](https://github.com/IntGenomicsLab/lrsomatic/actions/workflows/linting.yml/badge.svg)](https://github.com/IntGenomicsLab/lrsomatic/actions/workflows/linting.yml)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.17751829-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.17751829)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n\n[![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.10.4-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)\n[![nf-core template version](https://img.shields.io/badge/nf--core_template-4.1.0-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/4.1.0)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/IntGenomicsLab/lrsomatic)\n\n## Introduction\n\n**IntGenomicsLab/lrsomatic** is a robust bioinformatics pipeline designed for processing and analyzing **somatic DNA sequencing** data for long-read sequencing technologies from **Oxford Nanopore** and **PacBio**. It supports both canonical base DNA and modified base calling, including specialized applications such as **Fiber-seq**.\n\nThis **end-to-end pipeline** handles the entire workflow — **from raw read processing and alignment, to comprehensive somatic variant calling**, including single nucleotide variants, indels, structural variants, copy number alterations, and modified bases.\n\nIt can be run in both **matched tumour-normal** and **tumour-only mode**, offering flexibility depending on the users study design.\n\nDeveloped using **Nextflow DSL2**, it offers high portability and scalability across diverse computing environments. By leveraging Docker or Singularity containers, installation is streamlined and results are highly reproducible. Each process runs in an isolated container, simplifying dependency management and updates. Where applicable, pipeline components are sourced from **nf-core/modules**, promoting reuse, interoperability, and consistency within the broader Nextflow and nf-core ecosystems.\n\nFor more information on how to run the pipeline, you can also go [here](https://intgenomicslab.github.io/lrsomatic).\n\n## Pipeline summary\n\n![image](./assets/lrsomatic_1.0.png)\n\n**1) Pre-processing:**\n\na. Raw read QC ([`cramino`](https://github.com/wdecoster/cramino))\n\nb. Alignment to the reference genome ([`minimap2`](https://github.com/lh3/minimap2))\n\nc. Post alignment QC ([`cramino`](https://github.com/wdecoster/cramino), [`samtools idxstats`](https://github.com/samtools/samtools), [`samtools flagstats`](https://github.com/samtools/samtools), [`samtools stats`](https://github.com/samtools/samtools))\n\nd. Specific for calling modified base calling ([`Modkit`](https://github.com/nanoporetech/modkit), [`Fibertools`](https://github.com/fiberseq/fibertools-rs))\n\n**2i) Matched mode: small variant calling:**\n\na. Calling Germline SNPs ([`Clair3`](https://github.com/HKU-BAL/Clair3))\n\nb. Phasing and Haplotagging the SNPs in the normal and tumour BAM ([`LongPhase`](https://github.com/twolinin/longphase))\n\nc. Calling somatic SNVs ([`ClairS`](https://github.com/HKU-BAL/ClairS))\n\n**2ii) Tumour only mode: small variant calling:**\n\na. Calling Germline SNPs and somatic SNVs ([`ClairS-TO`](https://github.com/HKU-BAL/ClairS-TO))\n\nb. Phasing and Haplotagging germline SNPs in tumour BAM ([`LongPhase`](https://github.com/twolinin/longphase))\n\n**3) Large variant calling:**\n\na. Somatic structural variant calling ([`Severus`](https://github.com/KolmogorovLab/Severus))\n\nb. Copy number alterion calling; long read version of ([`ASCAT`](https://github.com/VanLoo-lab/ascat))\n\n**4) Annotation:**\n\na. Small variant annotation ([`VEP`](https://github.com/Ensembl/ensembl-vep))\n\nb. Structural variant annotation ([`VEP`](https://github.com/Ensembl/ensembl-vep))\n\n\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```csv\nsample,bam_tumor,bam_normal,platform,sex,fiber\nsample1,tumour.bam,normal.bam,ont,female,n\nsample2,tumour.bam,,ont,female,y\nsample3,tumour.bam,,pb,male,n\nsample4,tumour.bam,normal.bam,pb,male,y\n```\n\nEach row represents a sample. The bam files should always be unaligned bam files. All fields except for `bam_normal` are required. If `bam_normal` is empty, the pipeline will run in tumour only mode. `platform` should be either `ont` or `pb` for Oxford Nanopore Sequencing or PacBio sequencing, respectively. `sex` refers to the biological sex of the sample and should be either `female` or `male`. Finally, `fiber` specifies whether your sample is Fiber-seq data or not and should have either `y` for Yes or `n` for No.\n\nNow, you can run the pipeline using:\n\n```bash\nnextflow run IntGenomicsLab/lrsomatic \\\n -profile \\\n --input samplesheet.csv \\\n --outdir \n```\n\nMore detail is given in our [usage documentation](/docs/usage.md)\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/running/run-pipelines#using-parameter-files).\n\n## Credits\n\nIntGenomicsLab/lr_somatic was originally written by Luuk Harbers, Robert Forsyth, Alexandra Pančíková, Marios Eftychiou, Ruben Cools, Laurens Lambrechts, and Jonas Demeulemeester.\n\n## Pipeline output\n\nThis pipeline produces a series of different output files. The main output is an aligned and phased tumour bam file. This bam file can be used by any typical downstream tool that uses bam files as input. Furthermore, we have sample-specific QC outputs from `cramino` (fastq), `cramino` (bam), `mosdepth`, `samtools` (stats/flagstat/idxstats), and optionally `fibertools`. Finally, we have a `multiqc` report from that combines the output from `mosdepth` and `samtools` into one html report.\n\nBesides QC and the aligned and phased bam file, we have output from (structural) variant and copy number callers, of which some are optional. The output from these variant callers can be found in their respective folders. For small and structural variant callers (`clairS`, `clairS-TO`, and `severus`) these will contain, among others, `vcf` files with called variants. For `ascat` these contain files with final copy number information and plots of the copy number profiles.\n\nExample output directory structure:\n\n```\n├── Sample 1\n│ ├── ascat\n│ ├── bamfiles\n│ ├── qc\n│ │ ├── tumor\n│ │ │ ├── cramino_aln\n│ │ │ ├── cramino_ubam\n│ │ │ ├── fibertoolsrs\n│ │ │ ├── mosdepth\n│ │ │ ├── samtools\n│ ├── variants\n│ │ ├──clairS-TO\n│ │ ├──severus\n│ ├── vep\n│ │ ├── germline\n│ │ ├── somatic\n│ │ ├── SVs\n│\n├── Sample 2\n│ ├── ascat\n│ ├── bamfiles\n│ ├── qc\n│ │ ├── tumor\n│ │ │ ├── cramino_aln\n│ │ │ ├── cramino_ubam\n│ │ │ ├── fibertoolsrs\n│ │ │ ├── mosdepth\n│ │ │ ├── samtools\n│ │ ├── normal\n│ │ │ ├── cramino_aln\n│ │ │ ├── cramino_ubam\n│ │ │ ├── fibertoolsrs\n│ │ │ ├── mosdepth\n│ │ │ ├── samtools\n│ ├── variants\n│ │ ├── clair3\n│ │ ├── clairS\n│ │ ├── severus\n│ ├── vep\n│ │ ├── germline\n│ │ ├── somatic\n│ │ ├── SVs\n├── pipeline_info\n```\n\nmore detail is given in our [output documentation](/docs/output.md)\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](docs/CONTRIBUTING.md).\n\n## Citations\n\nIf you use `IntGenomicsLab/lrsomatic` for your analysis, please cite it using the following:\n\n> LRSomatic: a highly scalable and robust pipeline for somatic variant calling in long-read sequencing data\n>\n> Robert A. Forsyth*, Luuk Harbers*, Amber Verhasselt, Ana-Lucía Rocha Iraizós, Sidi Yang, Joris Vande Velde, Christopher Davies, Nischalan Pillay, Laurens Lambrechts, Jonas Demeulemeester\n>\n> bioRxiv 2026.02.26.707772; doi: https://doi.org/10.64898/2026.02.26.707772\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 uses 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/main/LICENSE).\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": "# IntGenomicsLab/lrsomatic\n\n[![Open in GitHub Codespaces](https://img.shields.io/badge/Open_In_GitHub_Codespaces-black?labelColor=grey&logo=github)](https://github.com/codespaces/new/IntGenomicsLab/lrsomatic)\n[![GitHub Actions CI Status](https://github.com/IntGenomicsLab/lrsomatic/actions/workflows/nf-test.yml/badge.svg)](https://github.com/IntGenomicsLab/lrsomatic/actions/workflows/nf-test.yml)\n[![GitHub Actions Linting Status](https://github.com/IntGenomicsLab/lrsomatic/actions/workflows/linting.yml/badge.svg)](https://github.com/IntGenomicsLab/lrsomatic/actions/workflows/linting.yml)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.17751829-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.17751829)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n\n[![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.10.4-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)\n[![nf-core template version](https://img.shields.io/badge/nf--core_template-4.1.0-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/4.1.0)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/IntGenomicsLab/lrsomatic)\n\n## Introduction\n\n**IntGenomicsLab/lrsomatic** is a robust bioinformatics pipeline designed for processing and analyzing **somatic DNA sequencing** data for long-read sequencing technologies from **Oxford Nanopore** and **PacBio**. It supports both canonical base DNA and modified base calling, including specialized applications such as **Fiber-seq**.\n\nThis **end-to-end pipeline** handles the entire workflow — **from raw read processing and alignment, to comprehensive somatic variant calling**, including single nucleotide variants, indels, structural variants, copy number alterations, and modified bases.\n\nIt can be run in both **matched tumour-normal** and **tumour-only mode**, offering flexibility depending on the users study design.\n\nDeveloped using **Nextflow DSL2**, it offers high portability and scalability across diverse computing environments. By leveraging Docker or Singularity containers, installation is streamlined and results are highly reproducible. Each process runs in an isolated container, simplifying dependency management and updates. Where applicable, pipeline components are sourced from **nf-core/modules**, promoting reuse, interoperability, and consistency within the broader Nextflow and nf-core ecosystems.\n\nFor more information on how to run the pipeline, you can also go [here](https://intgenomicslab.github.io/lrsomatic).\n\n## Pipeline summary\n\n![image](./assets/lrsomatic_1.0.png)\n\n**1) Pre-processing:**\n\na. Raw read QC ([`cramino`](https://github.com/wdecoster/cramino))\n\nb. Alignment to the reference genome ([`minimap2`](https://github.com/lh3/minimap2))\n\nc. Post alignment QC ([`cramino`](https://github.com/wdecoster/cramino), [`samtools idxstats`](https://github.com/samtools/samtools), [`samtools flagstats`](https://github.com/samtools/samtools), [`samtools stats`](https://github.com/samtools/samtools))\n\nd. Specific for calling modified base calling ([`Modkit`](https://github.com/nanoporetech/modkit), [`Fibertools`](https://github.com/fiberseq/fibertools-rs))\n\n**2i) Matched mode: small variant calling:**\n\na. Calling Germline SNPs ([`Clair3`](https://github.com/HKU-BAL/Clair3))\n\nb. Phasing and Haplotagging the SNPs in the normal and tumour BAM ([`LongPhase`](https://github.com/twolinin/longphase))\n\nc. Calling somatic SNVs ([`ClairS`](https://github.com/HKU-BAL/ClairS))\n\n**2ii) Tumour only mode: small variant calling:**\n\na. Calling Germline SNPs and somatic SNVs ([`ClairS-TO`](https://github.com/HKU-BAL/ClairS-TO))\n\nb. Phasing and Haplotagging germline SNPs in tumour BAM ([`LongPhase`](https://github.com/twolinin/longphase))\n\n**3) Large variant calling:**\n\na. Somatic structural variant calling ([`Severus`](https://github.com/KolmogorovLab/Severus))\n\nb. Copy number alterion calling; long read version of ([`ASCAT`](https://github.com/VanLoo-lab/ascat))\n\n**4) Annotation:**\n\na. Small variant annotation ([`VEP`](https://github.com/Ensembl/ensembl-vep))\n\nb. Structural variant annotation ([`VEP`](https://github.com/Ensembl/ensembl-vep))\n\n\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```csv\nsample,bam_tumor,bam_normal,platform,sex,fiber\nsample1,tumour.bam,normal.bam,ont,female,n\nsample2,tumour.bam,,ont,female,y\nsample3,tumour.bam,,pb,male,n\nsample4,tumour.bam,normal.bam,pb,male,y\n```\n\nEach row represents a sample. The bam files should always be unaligned bam files. All fields except for `bam_normal` are required. If `bam_normal` is empty, the pipeline will run in tumour only mode. `platform` should be either `ont` or `pb` for Oxford Nanopore Sequencing or PacBio sequencing, respectively. `sex` refers to the biological sex of the sample and should be either `female` or `male`. Finally, `fiber` specifies whether your sample is Fiber-seq data or not and should have either `y` for Yes or `n` for No.\n\nNow, you can run the pipeline using:\n\n```bash\nnextflow run IntGenomicsLab/lrsomatic \\\n -profile \\\n --input samplesheet.csv \\\n --outdir \n```\n\nMore detail is given in our [usage documentation](/docs/usage.md)\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/running/run-pipelines#using-parameter-files).\n\n## Credits\n\nIntGenomicsLab/lr_somatic was originally written by Luuk Harbers, Robert Forsyth, Amber Verhasselt, Alexandra Pančíková, Marios Eftychiou, Ruben Cools, Laurens Lambrechts, and Jonas Demeulemeester.\n\n## Pipeline output\n\nThis pipeline produces a series of different output files. The main output is an aligned and phased tumour bam file. This bam file can be used by any typical downstream tool that uses bam files as input. Furthermore, we have sample-specific QC outputs from `cramino` (fastq), `cramino` (bam), `mosdepth`, `samtools` (stats/flagstat/idxstats), and optionally `fibertools`. Finally, we have a `multiqc` report from that combines the output from `mosdepth` and `samtools` into one html report.\n\nBesides QC and the aligned and phased bam file, we have output from (structural) variant and copy number callers, of which some are optional. The output from these variant callers can be found in their respective folders. For small and structural variant callers (`clairS`, `clairS-TO`, and `severus`) these will contain, among others, `vcf` files with called variants. For `ascat` these contain files with final copy number information and plots of the copy number profiles.\n\nExample output directory structure:\n\n```\n├── Sample 1\n│ ├── ascat\n│ ├── bamfiles\n│ ├── qc\n│ │ ├── tumor\n│ │ │ ├── cramino_aln\n│ │ │ ├── cramino_ubam\n│ │ │ ├── fibertoolsrs\n│ │ │ ├── mosdepth\n│ │ │ ├── samtools\n│ ├── variants\n│ │ ├──clairS-TO\n│ │ ├──severus\n│ ├── vep\n│ │ ├── germline\n│ │ ├── somatic\n│ │ ├── SVs\n│\n├── Sample 2\n│ ├── ascat\n│ ├── bamfiles\n│ ├── qc\n│ │ ├── tumor\n│ │ │ ├── cramino_aln\n│ │ │ ├── cramino_ubam\n│ │ │ ├── fibertoolsrs\n│ │ │ ├── mosdepth\n│ │ │ ├── samtools\n│ │ ├── normal\n│ │ │ ├── cramino_aln\n│ │ │ ├── cramino_ubam\n│ │ │ ├── fibertoolsrs\n│ │ │ ├── mosdepth\n│ │ │ ├── samtools\n│ ├── variants\n│ │ ├── clair3\n│ │ ├── clairS\n│ │ ├── severus\n│ ├── vep\n│ │ ├── germline\n│ │ ├── somatic\n│ │ ├── SVs\n├── pipeline_info\n```\n\nmore detail is given in our [output documentation](/docs/output.md)\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](docs/CONTRIBUTING.md).\n\n## Citations\n\nIf you use `IntGenomicsLab/lrsomatic` for your analysis, please cite it using the following:\n\n> LRSomatic: a highly scalable and robust pipeline for somatic variant calling in long-read sequencing data\n>\n> Robert A. Forsyth*, Luuk Harbers*, Amber Verhasselt, Ana-Lucía Rocha Iraizós, Sidi Yang, Joris Vande Velde, Christopher Davies, Nischalan Pillay, Laurens Lambrechts, Jonas Demeulemeester\n>\n> bioRxiv 2026.02.26.707772; doi: https://doi.org/10.64898/2026.02.26.707772\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 uses 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/main/LICENSE).\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" @@ -146,6 +146,11 @@ "@id": "https://orcid.org/0000-0002-2660-2478" } ], + "contributor": [ + { + "@id": "https://orcid.org/0009-0000-4447-9795" + } + ], "dateCreated": "", "dateModified": "2026-08-14T15:41:35Z", "dct:conformsTo": "https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE/", @@ -333,7 +338,7 @@ { "@id": "https://orcid.org/0000-0003-3910-6497", "@type": "Person", - "affiliation": "VIB Center for Cancer Biology, VIB, Leuven, Belgium", + "affiliation": "VIB Center for Cancer Biology, VIB, Leuven, Belgium; Laboratory of Integrative Cancer Genomics, Department of Oncology, KU Leuven, Leuven, Belgium; VIB Center for AI and Computational Biology, VIB, Leuven, Belgium", "email": "luuk.harbers@kuleuven.be", "name": "Luuk Harbers", "url": "https://github.com/ljwharbers" @@ -346,6 +351,14 @@ "name": "Robert Forsyth", "url": "https://github.com/robert-a-forsyth" }, + { + "@id": "https://orcid.org/0009-0000-4447-9795", + "@type": "Person", + "affiliation": "Laboratory for Genetics of Malignant Disorders, Department of Human Genetics, KU Leuven, Leuven, Belgium", + "email": "amber.verhasselt@kuleuven.be", + "name": "Amber Verhasselt", + "url": "https://github.com/AmberVerhasselt" + }, { "@id": "https://orcid.org/0000-0002-0693-132X", "@type": "Person", From f942ed13128714762e9b87318c1934d72bac9193 Mon Sep 17 00:00:00 2001 From: ljwharbers Date: Tue, 18 Aug 2026 14:59:18 +0200 Subject: [PATCH 5/6] fix: correct Laurens Lambrechts' github URL in manifest.contributors His `github` field was a copy of @MariosEft97's URL. Set it to https://github.com/laulambr (name and VIB affiliation match; the only GitHub account under that name) and mirrored the change into `ro-crate-metadata.json`. Co-Authored-By: Claude Opus 5 --- CHANGELOG.md | 1 + nextflow.config | 2 +- ro-crate-metadata.json | 2 +- 3 files changed, 3 insertions(+), 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index ce04fb44..dfa664aa 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -15,6 +15,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### `Fixed` - [#182](https://github.com/IntGenomicsLab/lrsomatic/pull/182) - Added `--vcf` to the default `vep_args` so VEP writes VCF output rather than its default tab-delimited format (@AmberVerhasselt). +- Corrected the `github` URL for Laurens Lambrechts in `manifest.contributors`, which was a copy of @MariosEft97's, to @laulambr. RO-Crate metadata updated to match. ## v1.1.0 - [2026-04-28] diff --git a/nextflow.config b/nextflow.config index b253829e..c97495a3 100644 --- a/nextflow.config +++ b/nextflow.config @@ -363,7 +363,7 @@ manifest { name: 'Laurens Lambrechts', affiliation: 'VIB Center for Cancer Biology, VIB, Leuven, Belgium; Laboratory of Integrative Cancer Genomics, Department of Oncology, KU Leuven, Leuven, Belgium; VIB Center for AI and Computational Biology, VIB, Leuven, Belgium; Laboratory of Multi-omic Integrative Bioinformatics, Department of Human Genetics, KU Leuven, Leuven, Belgium', email: 'laurens.lambrechts@kuleuven.be', - github: 'https://github.com/MariosEft97', + github: 'https://github.com/laulambr', contribution: ['author'], // List of contribution types ('author', 'maintainer' or 'contributor') orcid: 'https://orcid.org/0000-0002-1415-4591' ], diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json index 590f4219..826cd4ba 100644 --- a/ro-crate-metadata.json +++ b/ro-crate-metadata.json @@ -389,7 +389,7 @@ "affiliation": "VIB Center for Cancer Biology, VIB, Leuven, Belgium; Laboratory of Integrative Cancer Genomics, Department of Oncology, KU Leuven, Leuven, Belgium; VIB Center for AI and Computational Biology, VIB, Leuven, Belgium; Laboratory of Multi-omic Integrative Bioinformatics, Department of Human Genetics, KU Leuven, Leuven, Belgium", "email": "laurens.lambrechts@kuleuven.be", "name": "Laurens Lambrechts", - "url": "https://github.com/MariosEft97" + "url": "https://github.com/laulambr" }, { "@id": "https://orcid.org/0000-0002-2660-2478", From a5514546a50d1f72ff28fbcee66a8270d47bb397 Mon Sep 17 00:00:00 2001 From: ljwharbers Date: Tue, 18 Aug 2026 15:02:28 +0200 Subject: [PATCH 6/6] docs: align Laurens Lambrechts' affiliation with the other core contributors Uses the same three-part VIB CCB / LICG KU Leuven / VIB CAICB string that @ljwharbers and @robert-a-forsyth carry, dropping the Laboratory of Multi-omic Integrative Bioinformatics entry. Mirrored into `ro-crate-metadata.json`. Co-Authored-By: Claude Opus 5 --- CHANGELOG.md | 1 + nextflow.config | 2 +- ro-crate-metadata.json | 2 +- 3 files changed, 3 insertions(+), 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index dfa664aa..245a9a25 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -11,6 +11,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - Raised the minimum Nextflow version to `25.10.4`, following the template, and bumped the nf-test CI matrix to match. - Filled in the `manifest.contributors` `contribution` fields: @ljwharbers and @robert-a-forsyth as author and maintainer, all other contributors as author. Previously empty, which left the RO-Crate metadata without any authors. - Added @AmberVerhasselt to `manifest.contributors` as a contributor and to the README credits, and expanded @ljwharbers' affiliation to match the other core contributors. RO-Crate metadata updated to match. +- Set @laulambr's affiliation to the same three-part VIB/KU Leuven string as the other core contributors. ### `Fixed` diff --git a/nextflow.config b/nextflow.config index c97495a3..fe655262 100644 --- a/nextflow.config +++ b/nextflow.config @@ -361,7 +361,7 @@ manifest { ], [ name: 'Laurens Lambrechts', - affiliation: 'VIB Center for Cancer Biology, VIB, Leuven, Belgium; Laboratory of Integrative Cancer Genomics, Department of Oncology, KU Leuven, Leuven, Belgium; VIB Center for AI and Computational Biology, VIB, Leuven, Belgium; Laboratory of Multi-omic Integrative Bioinformatics, Department of Human Genetics, KU Leuven, Leuven, Belgium', + affiliation: 'VIB Center for Cancer Biology, VIB, Leuven, Belgium; Laboratory of Integrative Cancer Genomics, Department of Oncology, KU Leuven, Leuven, Belgium; VIB Center for AI and Computational Biology, VIB, Leuven, Belgium', email: 'laurens.lambrechts@kuleuven.be', github: 'https://github.com/laulambr', contribution: ['author'], // List of contribution types ('author', 'maintainer' or 'contributor') diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json index 826cd4ba..ac2bf7be 100644 --- a/ro-crate-metadata.json +++ b/ro-crate-metadata.json @@ -386,7 +386,7 @@ { "@id": "https://orcid.org/0000-0002-1415-4591", "@type": "Person", - "affiliation": "VIB Center for Cancer Biology, VIB, Leuven, Belgium; Laboratory of Integrative Cancer Genomics, Department of Oncology, KU Leuven, Leuven, Belgium; VIB Center for AI and Computational Biology, VIB, Leuven, Belgium; Laboratory of Multi-omic Integrative Bioinformatics, Department of Human Genetics, KU Leuven, Leuven, Belgium", + "affiliation": "VIB Center for Cancer Biology, VIB, Leuven, Belgium; Laboratory of Integrative Cancer Genomics, Department of Oncology, KU Leuven, Leuven, Belgium; VIB Center for AI and Computational Biology, VIB, Leuven, Belgium", "email": "laurens.lambrechts@kuleuven.be", "name": "Laurens Lambrechts", "url": "https://github.com/laulambr"