diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json index 97c8c97f..237c9ed0 100644 --- a/.devcontainer/devcontainer.json +++ b/.devcontainer/devcontainer.json @@ -1,4 +1,5 @@ { + "$schema": "https://raw.githubusercontent.com/devcontainers/spec/main/schemas/devContainer.schema.json", "name": "nfcore", "image": "nfcore/devcontainer:latest", diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md deleted file mode 100644 index e357adf5..00000000 --- a/.github/CONTRIBUTING.md +++ /dev/null @@ -1,125 +0,0 @@ -# `nf-core/phaseimpute`: Contributing Guidelines - -Hi there! -Many thanks for taking an interest in improving nf-core/phaseimpute. - -We try to manage the required tasks for nf-core/phaseimpute using GitHub issues, you probably came to this page when creating one. -Please use the pre-filled template to save time. - -However, don't be put off by this template - other more general issues and suggestions are welcome! -Contributions to the code are even more welcome ;) - -> [!NOTE] -> If you need help using or modifying nf-core/phaseimpute then the best place to ask is on the nf-core Slack [#phaseimpute](https://nfcore.slack.com/channels/phaseimpute) channel ([join our Slack here](https://nf-co.re/join/slack)). - -## Contribution workflow - -If you'd like to write some code for nf-core/phaseimpute, the standard workflow is as follows: - -1. Check that there isn't already an issue about your idea in the [nf-core/phaseimpute issues](https://github.com/nf-core/phaseimpute/issues) to avoid duplicating work. If there isn't one already, please create one so that others know you're working on this -2. [Fork](https://help.github.com/en/github/getting-started-with-github/fork-a-repo) the [nf-core/phaseimpute repository](https://github.com/nf-core/phaseimpute) to your GitHub account -3. Make the necessary changes / additions within your forked repository following [Pipeline conventions](#pipeline-contribution-conventions) -4. Use `nf-core pipelines schema build` and add any new parameters to the pipeline JSON schema (requires [nf-core tools](https://github.com/nf-core/tools) >= 1.10). -5. Submit a Pull Request against the `dev` branch and wait for the code to be reviewed and merged - -If you're not used to this workflow with git, you can start with some [docs from GitHub](https://help.github.com/en/github/collaborating-with-issues-and-pull-requests) or even their [excellent `git` resources](https://try.github.io/). - -## Tests - -You have the option to test your changes locally by running the pipeline. For receiving warnings about process selectors and other `debug` information, it is recommended to use the debug profile. Execute all the tests with the following command: - -```bash -nf-test test --profile debug,test,docker --verbose -``` - -When you create a pull request with changes, [GitHub Actions](https://github.com/features/actions) will run automatic tests. -Typically, pull-requests are only fully reviewed when these tests are passing, though of course we can help out before then. - -There are typically two types of tests that run: - -### Lint tests - -`nf-core` has a [set of guidelines](https://nf-co.re/developers/guidelines) which all pipelines must adhere to. -To enforce these and ensure that all pipelines stay in sync, we have developed a helper tool which runs checks on the pipeline code. This is in the [nf-core/tools repository](https://github.com/nf-core/tools) and once installed can be run locally with the `nf-core pipelines lint ` command. - -If any failures or warnings are encountered, please follow the listed URL for more documentation. - -### Pipeline tests - -Each `nf-core` pipeline should be set up with a minimal set of test-data. -`GitHub Actions` then runs the pipeline on this data to ensure that it exits successfully. -If there are any failures then the automated tests fail. -These tests are run both with the latest available version of `Nextflow` and also the minimum required version that is stated in the pipeline code. - -## Patch - -:warning: Only in the unlikely and regretful event of a release happening with a bug. - -- On your own fork, make a new branch `patch` based on `upstream/main` or `upstream/master`. -- Fix the bug, and bump version (X.Y.Z+1). -- Open a pull-request from `patch` to `main`/`master` with the changes. - -## Getting help - -For further information/help, please consult the [nf-core/phaseimpute documentation](https://nf-co.re/phaseimpute/usage) and don't hesitate to get in touch on the nf-core Slack [#phaseimpute](https://nfcore.slack.com/channels/phaseimpute) channel ([join our Slack here](https://nf-co.re/join/slack)). - -## Pipeline contribution conventions - -To make the `nf-core/phaseimpute` code and processing logic more understandable for new contributors and to ensure quality, we semi-standardise the way the code and other contributions are written. - -### Adding a new step - -If you wish to contribute a new step, please use the following coding standards: - -1. Define the corresponding input channel into your new process from the expected previous process channel. -2. Write the process block (see below). -3. Define the output channel if needed (see below). -4. Add any new parameters to `nextflow.config` with a default (see below). -5. Add any new parameters to `nextflow_schema.json` with help text (via the `nf-core pipelines schema build` tool). -6. Add sanity checks and validation for all relevant parameters. -7. Perform local tests to validate that the new code works as expected. -8. If applicable, add a new test in the `tests` directory. -9. Update MultiQC config `assets/multiqc_config.yml` so relevant suffixes, file name clean up and module plots are in the appropriate order. If applicable, add a [MultiQC](https://https://multiqc.info/) module. -10. Add a description of the output files and if relevant any appropriate images from the MultiQC report to `docs/output.md`. - -### Default values - -Parameters should be initialised / defined with default values within the `params` scope in `nextflow.config`. - -Once there, use `nf-core pipelines schema build` to add to `nextflow_schema.json`. - -### Default processes resource requirements - -Sensible defaults for process resource requirements (CPUs / memory / time) for a process should be defined in `conf/base.config`. These should generally be specified generic with `withLabel:` selectors so they can be shared across multiple processes/steps of the pipeline. A nf-core standard set of labels that should be followed where possible can be seen in the [nf-core pipeline template](https://github.com/nf-core/tools/blob/main/nf_core/pipeline-template/conf/base.config), which has the default process as a single core-process, and then different levels of multi-core configurations for increasingly large memory requirements defined with standardised labels. - -The process resources can be passed on to the tool dynamically within the process with the `${task.cpus}` and `${task.memory}` variables in the `script:` block. - -### Naming schemes - -Please use the following naming schemes, to make it easy to understand what is going where. - -- initial process channel: `ch_output_from_` -- intermediate and terminal channels: `ch__for_` - -### Nextflow version bumping - -If you are using a new feature from core Nextflow, you may bump the minimum required version of nextflow in the pipeline with: `nf-core pipelines bump-version --nextflow . [min-nf-version]` - -### Images and figures - -For overview images and other documents we follow the nf-core [style guidelines and examples](https://nf-co.re/developers/design_guidelines). - -## GitHub Codespaces - -This repo includes a devcontainer configuration which will create a GitHub Codespaces for Nextflow development! This is an online developer environment that runs in your browser, complete with VSCode and a terminal. - -To get started: - -- Open the repo in [Codespaces](https://github.com/nf-core/phaseimpute/codespaces) -- Tools installed - - nf-core - - Nextflow - -Devcontainer specs: - -- [DevContainer config](.devcontainer/devcontainer.json) diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md index a7189a7e..7f4d9e6f 100644 --- a/.github/PULL_REQUEST_TEMPLATE.md +++ b/.github/PULL_REQUEST_TEMPLATE.md @@ -8,14 +8,14 @@ These are the most common things requested on pull requests (PRs). Remember that PRs should be made against the dev branch, unless you're preparing a pipeline release. -Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/phaseimpute/tree/main/.github/CONTRIBUTING.md) +Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/phaseimpute/tree/main/docs/CONTRIBUTING.md) --> ## 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/nf-core/phaseimpute/tree/main/.github/CONTRIBUTING.md) +- [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/phaseimpute/tree/main/docs/CONTRIBUTING.md) - [ ] If necessary, also make a PR on the nf-core/phaseimpute _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository. - [ ] Make sure your code lints (`nf-core pipelines lint`). - [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --outdir `). diff --git a/.github/actions/get-shards/action.yml b/.github/actions/get-shards/action.yml index 34085279..e2833ee9 100644 --- a/.github/actions/get-shards/action.yml +++ b/.github/actions/get-shards/action.yml @@ -21,7 +21,7 @@ runs: using: "composite" steps: - name: Install nf-test - uses: nf-core/setup-nf-test@v1 + uses: nf-core/setup-nf-test@4069fbbaabe94c08faba4ad261bfa88225ba133f # v2 with: version: ${{ env.NFT_VER }} - name: Get number of shards diff --git a/.github/actions/nf-test/action.yml b/.github/actions/nf-test/action.yml index 3b9724c7..ad686e8e 100644 --- a/.github/actions/nf-test/action.yml +++ b/.github/actions/nf-test/action.yml @@ -20,24 +20,24 @@ runs: using: "composite" steps: - name: Setup Nextflow - uses: nf-core/setup-nextflow@v2 + uses: nf-core/setup-nextflow@b4ec1bc7c16a94435159de94a05253542fddf6ef # v3 with: version: "${{ env.NXF_VERSION }}" - name: Set up Python - uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6 + uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6 with: python-version: "3.14" - name: Install nf-test - uses: nf-core/setup-nf-test@v1 + uses: nf-core/setup-nf-test@4069fbbaabe94c08faba4ad261bfa88225ba133f # v2 with: version: "${{ env.NFT_VER }}" install-pdiff: true - name: Setup apptainer if: contains(inputs.profile, 'singularity') - uses: eWaterCycle/setup-apptainer@main + uses: eWaterCycle/setup-apptainer@3f706d898c9db585b1d741b4692e66755f3a1b40 # v2 - name: Set up Singularity if: contains(inputs.profile, 'singularity') @@ -48,7 +48,7 @@ runs: - name: Conda setup if: contains(inputs.profile, 'conda') - uses: conda-incubator/setup-miniconda@505e6394dae86d6a5c7fbb6e3fb8938e3e863830 # v3 + uses: conda-incubator/setup-miniconda@8ee1f361103df19b6f8c8655fd3967a8ecb162d5 # v4 with: auto-update-conda: true conda-solver: libmamba diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml index 826e0b20..d01c09b1 100644 --- a/.github/workflows/awsfulltest.yml +++ b/.github/workflows/awsfulltest.yml @@ -23,21 +23,40 @@ jobs: echo "revision=${{ (github.event_name == 'workflow_dispatch' || github.event_name == 'release') && github.sha || 'dev' }}" >> "$GITHUB_OUTPUT" - name: Launch workflow via Seqera Platform - uses: seqeralabs/action-tower-launch@v2 + uses: seqeralabs/action-tower-launch@51565b514bff1827cf34620de25d0055759f1fc9 # v2 with: workspace_id: ${{ vars.TOWER_WORKSPACE_ID }} access_token: ${{ secrets.TOWER_ACCESS_TOKEN }} compute_env: ${{ vars.TOWER_COMPUTE_ENV }} revision: ${{ steps.revision.outputs.revision }} workdir: s3://${{ vars.AWS_S3_BUCKET }}/work/phaseimpute/work-${{ steps.revision.outputs.revision }} + nextflow_config: | + plugins { + id 'nf-slack@0.5.0' + } + slack { + enabled = true + bot { + token = '${{ secrets.NFSLACK_BOT_TOKEN }}' + channel = 'phaseimpute' + } + onStart { + enabled = false + } + onComplete { + message = ':white_check_mark: *phaseimpute/test_full* completed successfully! :tada:' + } + onError { + message = ':x: *phaseimpute/test_full* failed :crying_cat_face:' + } + } parameters: | { - "hook_url": "${{ secrets.MEGATESTS_ALERTS_SLACK_HOOK_URL }}", "outdir": "s3://${{ vars.AWS_S3_BUCKET }}/phaseimpute/results-${{ steps.revision.outputs.revision }}" } profiles: test_full - - uses: actions/upload-artifact@330a01c490aca151604b8cf639adc76d48f6c5d4 # v5 + - uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7 with: name: Seqera Platform debug log file path: | diff --git a/.github/workflows/awstest.yml b/.github/workflows/awstest.yml index 27284429..b3900639 100644 --- a/.github/workflows/awstest.yml +++ b/.github/workflows/awstest.yml @@ -12,7 +12,7 @@ jobs: steps: # Launch workflow using Seqera Platform CLI tool action - name: Launch workflow via Seqera Platform - uses: seqeralabs/action-tower-launch@v2 + uses: seqeralabs/action-tower-launch@51565b514bff1827cf34620de25d0055759f1fc9 # v2 with: workspace_id: ${{ vars.TOWER_WORKSPACE_ID }} access_token: ${{ secrets.TOWER_ACCESS_TOKEN }} @@ -25,7 +25,7 @@ jobs: } profiles: test - - uses: actions/upload-artifact@330a01c490aca151604b8cf639adc76d48f6c5d4 # v5 + - uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7 with: name: Seqera Platform debug log file path: | diff --git a/.github/workflows/branch.yml b/.github/workflows/branch.yml index 30076fc1..10d5448f 100644 --- a/.github/workflows/branch.yml +++ b/.github/workflows/branch.yml @@ -21,7 +21,7 @@ jobs: # NOTE - this doesn't currently work if the PR is coming from a fork, due to limitations in GitHub actions secrets - name: Post PR comment if: failure() - uses: mshick/add-pr-comment@b8f338c590a895d50bcbfa6c5859251edc8952fc # v2 + uses: mshick/add-pr-comment@8e4927817251f1ff60c001f04568532b38e0b4a0 # v3 with: message: | ## This PR is against the `${{github.event.pull_request.base.ref}}` branch :x: diff --git a/.github/workflows/clean-up.yml b/.github/workflows/clean-up.yml index 6adb0fff..172de6f3 100644 --- a/.github/workflows/clean-up.yml +++ b/.github/workflows/clean-up.yml @@ -10,7 +10,7 @@ jobs: issues: write pull-requests: write steps: - - uses: actions/stale@5f858e3efba33a5ca4407a664cc011ad407f2008 # v10 + - uses: actions/stale@b5d41d4e1d5dceea10e7104786b73624c18a190f # v10 with: stale-issue-message: "This issue has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor. Remove stale label or add a comment otherwise this issue will be closed in 20 days." stale-pr-message: "This PR has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor. Remove stale label or add a comment if it is still useful." diff --git a/.github/workflows/download_pipeline.yml b/.github/workflows/download_pipeline.yml index 45884ff9..a7bf4fc2 100644 --- a/.github/workflows/download_pipeline.yml +++ b/.github/workflows/download_pipeline.yml @@ -38,13 +38,16 @@ jobs: runs-on: ubuntu-latest needs: configure steps: + - name: Check out pipeline code + uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6 + - name: Install Nextflow - uses: nf-core/setup-nextflow@v2 + uses: nf-core/setup-nextflow@b4ec1bc7c16a94435159de94a05253542fddf6ef # v3 - name: Disk space cleanup uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1 - - uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6 + - uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6 with: python-version: "3.14" architecture: "x64" @@ -54,10 +57,15 @@ jobs: with: apptainer-version: 1.3.4 + - name: Read .nf-core.yml + id: read_yml + run: | + echo "nf_core_version=$(yq '.nf_core_version' ${{ github.workspace }}/.nf-core.yml)" >> "$GITHUB_OUTPUT" + - name: Install dependencies run: | python -m pip install --upgrade pip - pip install git+https://github.com/nf-core/tools.git + pip install nf-core==${{ steps.read_yml.outputs['nf_core_version'] }} - name: Make a cache directory for the container images run: | @@ -127,7 +135,7 @@ jobs: fi - name: Upload Nextflow logfile for debugging purposes - uses: actions/upload-artifact@330a01c490aca151604b8cf639adc76d48f6c5d4 # v5 + uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7 with: name: nextflow_logfile.txt path: .nextflow.log* diff --git a/.github/workflows/fix_linting.yml b/.github/workflows/fix_linting.yml index 395b65dc..56e3cda1 100644 --- a/.github/workflows/fix_linting.yml +++ b/.github/workflows/fix_linting.yml @@ -13,7 +13,7 @@ jobs: runs-on: ubuntu-latest steps: # Use the @nf-core-bot token to check out so we can push later - - uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5 + - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6 with: token: ${{ secrets.nf_core_bot_auth_token }} @@ -31,22 +31,18 @@ jobs: env: GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }} - # Install and run pre-commit - - uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6 - with: - python-version: "3.14" - - - name: Install pre-commit - run: pip install pre-commit + - name: Install Nextflow + uses: nf-core/setup-nextflow@b4ec1bc7c16a94435159de94a05253542fddf6ef # v3 - - name: Run pre-commit - id: pre-commit - run: pre-commit run --all-files + # Install and run prek + - name: Run prek + id: prek + uses: j178/prek-action@6ad80277337ad479fe43bd70701c3f7f8aa74db3 # v2 continue-on-error: true # indication that the linting has finished - name: react if linting finished succesfully - if: steps.pre-commit.outcome == 'success' + if: steps.prek.outcome == 'success' uses: peter-evans/create-or-update-comment@e8674b075228eee787fea43ef493e45ece1004c9 # v5 with: comment-id: ${{ github.event.comment.id }} @@ -54,7 +50,7 @@ jobs: - name: Commit & push changes id: commit-and-push - if: steps.pre-commit.outcome == 'failure' + if: steps.prek.outcome == 'failure' run: | git config user.email "core@nf-co.re" git config user.name "nf-core-bot" diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml index 7a527a34..8738ffc9 100644 --- a/.github/workflows/linting.yml +++ b/.github/workflows/linting.yml @@ -11,33 +11,31 @@ jobs: pre-commit: runs-on: ubuntu-latest steps: - - uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5 + - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6 - - name: Set up Python 3.14 - uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6 - with: - python-version: "3.14" - - - name: Install pre-commit - run: pip install pre-commit + - name: Install Nextflow + uses: nf-core/setup-nextflow@b4ec1bc7c16a94435159de94a05253542fddf6ef # v3 - - name: Run pre-commit - run: pre-commit run --all-files + - name: Run prek + uses: j178/prek-action@6ad80277337ad479fe43bd70701c3f7f8aa74db3 # v2 nf-core: runs-on: ubuntu-latest steps: - name: Check out pipeline code - uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5 + uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6 - name: Install Nextflow - uses: nf-core/setup-nextflow@v2 + uses: nf-core/setup-nextflow@b4ec1bc7c16a94435159de94a05253542fddf6ef # v3 - - uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6 + - uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6 with: python-version: "3.14" architecture: "x64" + - name: Setup uv + uses: astral-sh/setup-uv@08807647e7069bb48b6ef5acd8ec9567f424441b # v8.1.0 + - name: read .nf-core.yml uses: pietrobolcato/action-read-yaml@9f13718d61111b69f30ab4ac683e67a56d254e1d # 1.1.0 id: read_yml @@ -45,12 +43,10 @@ jobs: config: ${{ github.workspace }}/.nf-core.yml - name: Install dependencies - run: | - python -m pip install --upgrade pip - pip install nf-core==${{ steps.read_yml.outputs['nf_core_version'] }} + run: uv tool install nf-core==${{ steps.read_yml.outputs['nf_core_version'] }} - name: Run nf-core pipelines lint - if: ${{ github.base_ref != 'master' }} + if: ${{ github.base_ref != 'master' || github.base_ref != 'main' }} env: GITHUB_COMMENTS_URL: ${{ github.event.pull_request.comments_url }} GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} @@ -58,7 +54,7 @@ jobs: run: nf-core -l lint_log.txt pipelines lint --dir ${GITHUB_WORKSPACE} --markdown lint_results.md - name: Run nf-core pipelines lint --release - if: ${{ github.base_ref == 'master' }} + if: ${{ github.base_ref == 'master' || github.base_ref == 'main' }} env: GITHUB_COMMENTS_URL: ${{ github.event.pull_request.comments_url }} GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} @@ -71,7 +67,7 @@ jobs: - name: Upload linting log file artifact if: ${{ always() }} - uses: actions/upload-artifact@330a01c490aca151604b8cf639adc76d48f6c5d4 # v5 + uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7 with: name: linting-logs path: | diff --git a/.github/workflows/linting_comment.yml b/.github/workflows/linting_comment.yml index e6e9bc26..5b0c24f7 100644 --- a/.github/workflows/linting_comment.yml +++ b/.github/workflows/linting_comment.yml @@ -11,7 +11,7 @@ jobs: runs-on: ubuntu-latest steps: - name: Download lint results - uses: dawidd6/action-download-artifact@ac66b43f0e6a346234dd65d4d0c8fbb31cb316e5 # v11 + uses: dawidd6/action-download-artifact@b6e2e70617bc3265edd6dab6c906732b2f1ae151 # v21 with: workflow: linting.yml workflow_conclusion: completed @@ -21,7 +21,7 @@ jobs: run: echo "pr_number=$(cat linting-logs/PR_number.txt)" >> $GITHUB_OUTPUT - name: Post PR comment - uses: marocchino/sticky-pull-request-comment@773744901bac0e8cbb5a0dc842800d45e9b2b405 # v2 + uses: marocchino/sticky-pull-request-comment@70d2764d1a7d5d9560b100cbea0077fc8f633987 # v3 with: GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} number: ${{ steps.pr_number.outputs.pr_number }} diff --git a/.github/workflows/nf-test.yml b/.github/workflows/nf-test.yml index 553105b1..efd72d65 100644 --- a/.github/workflows/nf-test.yml +++ b/.github/workflows/nf-test.yml @@ -40,7 +40,7 @@ jobs: rm -rf ./* || true rm -rf ./.??* || true ls -la ./ - - uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5 + - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6 with: fetch-depth: 0 @@ -78,14 +78,14 @@ jobs: - isMain: false profile: "singularity" NXF_VER: - - "25.10.0" + - "25.10.4" - "latest-everything" env: NXF_ANSI_LOG: false TOTAL_SHARDS: ${{ needs.nf-test-changes.outputs.total_shards }} steps: - - uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5 + - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6 with: fetch-depth: 0 diff --git a/.github/workflows/release-announcements.yml b/.github/workflows/release-announcements.yml index 431d3d44..78d5dbe0 100644 --- a/.github/workflows/release-announcements.yml +++ b/.github/workflows/release-announcements.yml @@ -18,7 +18,7 @@ jobs: id: get_description run: | echo "description=$(curl -s https://nf-co.re/pipelines.json | jq -r '.remote_workflows[] | select(.full_name == "${{ github.repository }}") | .description')" >> $GITHUB_OUTPUT - - uses: rzr/fediverse-action@master + - uses: rzr/fediverse-action@563159eb8d45f70ab6aaba36ed55cd037e51f441 # master with: access-token: ${{ secrets.MASTODON_ACCESS_TOKEN }} host: "mstdn.science" # custom host if not "mastodon.social" (default) @@ -34,7 +34,7 @@ jobs: bsky-post: runs-on: ubuntu-latest steps: - - uses: zentered/bluesky-post-action@6461056ea355ea43b977e149f7bf76aaa572e5e8 # v0.3.0 + - uses: zentered/bluesky-post-action@5a91cc2ad10a304a4e96c16182dbe4918710bcf6 # v0.4.0 with: post: | Pipeline release! ${{ github.repository }} v${{ github.event.release.tag_name }} - ${{ github.event.release.name }}! diff --git a/.github/workflows/template-version-comment.yml b/.github/workflows/template-version-comment.yml index e8560fc7..ea30827e 100644 --- a/.github/workflows/template-version-comment.yml +++ b/.github/workflows/template-version-comment.yml @@ -9,7 +9,7 @@ jobs: runs-on: ubuntu-latest steps: - name: Check out pipeline code - uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5 + uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6 with: ref: ${{ github.event.pull_request.head.sha }} @@ -29,7 +29,7 @@ jobs: run: echo "OUTPUT=$(pip list --outdated | grep nf-core)" >> ${GITHUB_ENV} - name: Post nf-core template version comment - uses: mshick/add-pr-comment@b8f338c590a895d50bcbfa6c5859251edc8952fc # v2 + uses: mshick/add-pr-comment@8e4927817251f1ff60c001f04568532b38e0b4a0 # v3 if: | contains(env.OUTPUT, 'nf-core') with: @@ -42,5 +42,5 @@ jobs: > Your pipeline is using an old version of the nf-core template: ${{ steps.read_yml.outputs['nf_core_version'] }}. > Please update your pipeline to the latest version. > - > For more documentation on how to update your pipeline, please see the [nf-core documentation](https://github.com/nf-core/tools?tab=readme-ov-file#sync-a-pipeline-with-the-template) and [Synchronisation documentation](https://nf-co.re/docs/contributing/sync). + > For more documentation on how to update your pipeline, please see the [Synchronisation documentation](https://nf-co.re/docs/developing/template-syncs/overview). # diff --git a/.gitignore b/.gitignore index 3d4a629b..b53389df 100644 --- a/.gitignore +++ b/.gitignore @@ -7,6 +7,7 @@ testing/ testing* *.pyc null/ +.lineage/ *.code-workspace .nf-test* *.xml.bkp diff --git a/.nf-core.yml b/.nf-core.yml index cff72e0c..a326ebb3 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -1,8 +1,8 @@ lint: - nf_test_content: false files_unchanged: - .github/PULL_REQUEST_TEMPLATE.md -nf_core_version: 3.5.2 + nf_test_content: false +nf_core_version: 4.0.2 repository_type: pipeline template: author: Louis Le Nezet, Anabella Trigila diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index d06777a8..f51e1a28 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -4,7 +4,7 @@ repos: hooks: - id: prettier additional_dependencies: - - prettier@3.6.2 + - prettier@3.8.3 - repo: https://github.com/pre-commit/pre-commit-hooks rev: v6.0.0 hooks: @@ -13,15 +13,21 @@ repos: exclude: | (?x)^( .*ro-crate-metadata.json$| - modules/nf-core/.*| - subworkflows/nf-core/.*| + modules/(?!local/).*| + subworkflows/(?!local/).*| .*\.snap$ )$ - id: end-of-file-fixer exclude: | (?x)^( .*ro-crate-metadata.json$| - modules/nf-core/.*| - subworkflows/nf-core/.*| + modules/(?!local/).*| + subworkflows/(?!local/).*| .*\.snap$ )$ + - repo: https://github.com/seqeralabs/nf-lint-pre-commit + rev: v0.3.0 + hooks: + - id: nextflow-lint + files: '\.nf$|nextflow\.config$' + args: ["-output", "json"] diff --git a/.prettierignore b/.prettierignore index dd749d43..63cde500 100644 --- a/.prettierignore +++ b/.prettierignore @@ -1,6 +1,4 @@ email_template.html -adaptivecard.json -slackreport.json .nextflow* work/ data/ diff --git a/CHANGELOG.md b/CHANGELOG.md index 2f921caa..279c9b75 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,7 +3,7 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). -## v1.2.0dev +## v1.2.0dev - [date] ### `Added` @@ -37,6 +37,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [#273](https://github.com/nf-core/phaseimpute/pull/273) - Update nf-core modules, fix syntax. Remove `SAMTOOLS_REHEADER` patch and pass command through meta map. Update nf-test in Github Action to 0.9.4. - [#276](https://github.com/nf-core/phaseimpute/pull/276) - Migrate all `params.value` usage to entry workflow. Use groovy map to store parameters for each step. Use nextflow 25.10 for `getGenomeAttribute()`. - [#286](https://github.com/nf-core/phaseimpute/pull/286) - Remove unecessary `saveAs` from config thanks to topic migration. +- [#291](https://github.com/nf-core/phaseimpute/pull/291) - Update TEMPLATE to nf-core tools version 4.0.2. ### `Fixed` @@ -54,7 +55,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 | `bedtools` | 2.31.1 | No longer used | | `samtools` | 1.22.1 | 1.23 | | `gawk` | 5.3.0 | 5.3.1 | -| `multiqc` | 1.32 | 1.33 | +| `multiqc` | 1.32 | 1.35 | ### New contributors diff --git a/README.md b/README.md index 95f55564..b757e600 100644 --- a/README.md +++ b/README.md @@ -10,8 +10,8 @@ [![GitHub Actions Linting Status](https://github.com/nf-core/phaseimpute/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/phaseimpute/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/phaseimpute/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.14329225-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.14329225) [![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%A525.10.0-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/) -[![nf-core template version](https://img.shields.io/badge/nf--core_template-3.5.1-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.5.1) +[![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-4.0.2-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/4.0.2) [![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/) [![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/) [![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/) @@ -52,7 +52,7 @@ For more detailed instructions, please refer to the [usage documentation](https: ## Usage > [!NOTE] -> 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. +> 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. The primary function of this pipeline is to impute a target dataset based on a phased panel. Begin by preparing a samplesheet with your input data, formatted as follows: @@ -83,7 +83,7 @@ nextflow run nf-core/phaseimpute \ ``` > [!WARNING] -> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files). +> 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). For more details and further functionality, please refer to the [usage documentation](https://nf-co.re/phaseimpute/usage) and the [parameter documentation](https://nf-co.re/phaseimpute/parameters). @@ -106,7 +106,7 @@ We thank the following people for their extensive assistance in the development ## Contributions and Support -If you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md). Further development tips can be found in the [development documentation](docs/development.md). +If you would like to contribute to this pipeline, please see the [contributing guidelines](docs/CONTRIBUTING.md). Further development tips can be found in the [development documentation](docs/development.md). For further information or help, don't hesitate to get in touch on the [Slack `#phaseimpute` channel](https://nfcore.slack.com/channels/phaseimpute) (you can join with [this invite](https://nf-co.re/join/slack)). diff --git a/assets/adaptivecard.json b/assets/adaptivecard.json deleted file mode 100644 index e7079ad6..00000000 --- a/assets/adaptivecard.json +++ /dev/null @@ -1,67 +0,0 @@ -{ - "type": "message", - "attachments": [ - { - "contentType": "application/vnd.microsoft.card.adaptive", - "contentUrl": null, - "content": { - "\$schema": "http://adaptivecards.io/schemas/adaptive-card.json", - "msteams": { - "width": "Full" - }, - "type": "AdaptiveCard", - "version": "1.2", - "body": [ - { - "type": "TextBlock", - "size": "Large", - "weight": "Bolder", - "color": "<% if (success) { %>Good<% } else { %>Attention<%} %>", - "text": "nf-core/phaseimpute v${version} - ${runName}", - "wrap": true - }, - { - "type": "TextBlock", - "spacing": "None", - "text": "Completed at ${dateComplete} (duration: ${duration})", - "isSubtle": true, - "wrap": true - }, - { - "type": "TextBlock", - "text": "<% if (success) { %>Pipeline completed successfully!<% } else { %>Pipeline completed with errors. The full error message was: ${errorReport}.<% } %>", - "wrap": true - }, - { - "type": "TextBlock", - "text": "The command used to launch the workflow was as follows:", - "wrap": true - }, - { - "type": "TextBlock", - "text": "${commandLine}", - "isSubtle": true, - "wrap": true - } - ], - "actions": [ - { - "type": "Action.ShowCard", - "title": "Pipeline Configuration", - "card": { - "type": "AdaptiveCard", - "\$schema": "http://adaptivecards.io/schemas/adaptive-card.json", - "body": [ - { - "type": "FactSet", - "facts": [<% out << summary.collect{ k,v -> "{\"title\": \"$k\", \"value\" : \"$v\"}"}.join(",\n") %> - ] - } - ] - } - } - ] - } - } - ] -} diff --git a/assets/slackreport.json b/assets/slackreport.json deleted file mode 100644 index 264f3bed..00000000 --- a/assets/slackreport.json +++ /dev/null @@ -1,34 +0,0 @@ -{ - "attachments": [ - { - "fallback": "Plain-text summary of the attachment.", - "color": "<% if (success) { %>good<% } else { %>danger<%} %>", - "author_name": "nf-core/phaseimpute ${version} - ${runName}", - "author_icon": "https://www.nextflow.io/docs/latest/_static/favicon.ico", - "text": "<% if (success) { %>Pipeline completed successfully!<% } else { %>Pipeline completed with errors<% } %>", - "fields": [ - { - "title": "Command used to launch the workflow", - "value": "```${commandLine}```", - "short": false - } - <% - if (!success) { %> - , - { - "title": "Full error message", - "value": "```${errorReport}```", - "short": false - }, - { - "title": "Pipeline configuration", - "value": "<% out << summary.collect{ k,v -> k == "hook_url" ? "_${k}_: (_hidden_)" : ( ( v.class.toString().contains('Path') || ( v.class.toString().contains('String') && v.contains('/') ) ) ? "_${k}_: `${v}`" : (v.class.toString().contains('DateTime') ? ("_${k}_: " + v.format(java.time.format.DateTimeFormatter.ofLocalizedDateTime(java.time.format.FormatStyle.MEDIUM))) : "_${k}_: ${v}") ) }.join(",\n") %>", - "short": false - } - <% } - %> - ], - "footer": "Completed at <% out << dateComplete.format(java.time.format.DateTimeFormatter.ofLocalizedDateTime(java.time.format.FormatStyle.MEDIUM)) %> (duration: ${duration})" - } - ] -} diff --git a/conf/base.config b/conf/base.config index afb52143..89c30740 100644 --- a/conf/base.config +++ b/conf/base.config @@ -14,7 +14,7 @@ process { memory = { 6.GB * task.attempt } time = { 4.h * task.attempt } - errorStrategy = { task.exitStatus in ((130..145) + 104 + 175) ? 'retry' : 'finish' } + errorStrategy = { task.exitStatus in ((130..145) + 104 + (175..177)) ? 'retry' : 'finish' } maxRetries = 1 maxErrors = '-1' diff --git a/conf/containers_conda_lock_files_amd64.config b/conf/containers_conda_lock_files_amd64.config index f6b0997e..a05393e6 100644 --- a/conf/containers_conda_lock_files_amd64.config +++ b/conf/containers_conda_lock_files_amd64.config @@ -1 +1 @@ -process { withName: 'MULTIQC' { container = 'https://wave.seqera.io/v1alpha1/builds/bd-ee7739d47738383b_1/condalock' } } +process { withName: 'MULTIQC' { container = 'modules/nf-core/multiqc/.conda-lock/linux_amd64-bd-839587b417d23042_1.txt' } } diff --git a/conf/containers_conda_lock_files_arm64.config b/conf/containers_conda_lock_files_arm64.config index 0cd12a28..7b7f2b66 100644 --- a/conf/containers_conda_lock_files_arm64.config +++ b/conf/containers_conda_lock_files_arm64.config @@ -1 +1 @@ -process { withName: 'MULTIQC' { container = 'https://wave.seqera.io/v1alpha1/builds/bd-58d7dee710ab3aa8_1/condalock' } } +process { withName: 'MULTIQC' { container = 'modules/nf-core/multiqc/.conda-lock/linux_arm64-bd-3e45d17b40a576b4_1.txt' } } diff --git a/conf/containers_docker_amd64.config b/conf/containers_docker_amd64.config index dd93726b..66a4c027 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:1.33--ee7739d47738383b' } } +process { withName: 'MULTIQC' { container = 'community.wave.seqera.io/library/multiqc:1.35--839587b417d23042' } } diff --git a/conf/containers_docker_arm64.config b/conf/containers_docker_arm64.config index 23418fef..209188f0 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:1.33--58d7dee710ab3aa8' } } +process { withName: 'MULTIQC' { container = 'community.wave.seqera.io/library/multiqc:1.35--3e45d17b40a576b4' } } diff --git a/conf/containers_singularity_https_amd64.config b/conf/containers_singularity_https_amd64.config index d04c5be3..2465ec54 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/sha256/34/34e733a9ae16a27e80fe00f863ea1479c96416017f24a907996126283e7ecd4d/data' } } +process { withName: 'MULTIQC' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/12/1297c0f5075c19486da167ebf1b6136907d6b5339697b87b29fda335221785b3/data' } } diff --git a/conf/containers_singularity_https_arm64.config b/conf/containers_singularity_https_arm64.config index 4a031237..80ca27ed 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/sha256/78/78b89e91d89e9cc99ad5ade5be311f347838cb2acbfb4f13bc343b170be09ce4/data' } } +process { withName: 'MULTIQC' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/c0/c007304153702edc622f1a76b41505e7fca65c7145e5b8b2ddce62a5c59af207/data' } } diff --git a/conf/containers_singularity_oras_amd64.config b/conf/containers_singularity_oras_amd64.config index 2d8d51fc..19753cfe 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:1.33--e3576ddf588fa00d' } } +process { withName: 'MULTIQC' { container = 'oras://community.wave.seqera.io/library/multiqc:1.35--cb7458fda84d6393' } } diff --git a/conf/containers_singularity_oras_arm64.config b/conf/containers_singularity_oras_arm64.config index c3210dd0..e5439f67 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:1.33--2537ca5f8445e3c2' } } +process { withName: 'MULTIQC' { container = 'oras://community.wave.seqera.io/library/multiqc:1.35--f79e87603d312ac0' } } diff --git a/docs/CONTRIBUTING.md b/docs/CONTRIBUTING.md new file mode 100644 index 00000000..b82e4bb6 --- /dev/null +++ b/docs/CONTRIBUTING.md @@ -0,0 +1,185 @@ +--- +title: Contributing +markdownPlugin: checklist +--- + +# `nf-core/phaseimpute`: Contributing guidelines + +Hi there! +Thanks for taking an interest in improving nf-core/phaseimpute. + +This page describes the recommended nf-core way to contribute to both nf-core/phaseimpute 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 nf-core/phaseimpute. + +> [!NOTE] +> If you need help using or modifying nf-core/phaseimpute, ask on the nf-core Slack [#phaseimpute](https://nfcore.slack.com/channels/phaseimpute) channel ([join our Slack here](https://nf-co.re/join/slack)). + +## General contribution guidelines + +### Contribution quick start + +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/nf-core/phaseimpute/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 [nf-core/phaseimpute repository](https://github.com/nf-core/phaseimpute) 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`. +- [ ] Run and/or update tests. See [Testing](#testing) for more information. +- [ ] [Lint](#lint-tests) your code with nf-core/tools. +- [ ] Submit a pull request (PR) against the `dev` branch and request a review. + +If you are not used to this workflow with Git, see the [GitHub documentation](https://help.github.com/en/github/collaborating-with-issues-and-pull-requests) or [Git resources](https://try.github.io/) for more information. + +## Use of AI and LLMs + +The nf-core stance on the use of AI and LLMs is that humans are still ultimately responsible for their submitted code, regardless of the tools they use. + +If you’re using AI tools, try to stick by these guidelines: + +- Keep PRs as small and focussed as possible +- Avoid any unnecessary changes, such as moving or refactoring code (unless that is the explicit intention of the PR) +- Review all generated code yourself before opening a PR, and ensure that you understand it +- Engage with the community review process and expect to make revisions + +For more detail, see the the [blog post](https://nf-co.re/blog/2026/statement-on-ai) for a statement from the nf-core/core team. + +### Getting help + +For further information and help, see the [nf-core/phaseimpute documentation](https://nf-co.re/phaseimpute/usage) or ask on the nf-core [#phaseimpute](https://nfcore.slack.com/channels/phaseimpute) Slack channel ([join our Slack here](https://nf-co.re/join/slack)). + +### GitHub Codespaces + +You can contribute to nf-core/phaseimpute 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/nf-core/phaseimpute/codespaces). + +### Testing + +Once you have made your changes, run the pipeline with nf-test to test them locally. +For additional information, use the `--verbose` flag to view the Nextflow console log output. + +```bash +nf-test test --tag test --profile +docker --verbose +``` + +If you have added new functionality, ensure you update the test assertions in the `.nf.test` files in the `tests/` directory. +Update the snapshots with the following command: + +```bash +nf-test test --tag test --profile +docker --verbose --update-snapshots +``` + +When you create a pull request with changes, GitHub Actions will run automatic tests. +Pull requests are typically reviewed when these tests are passing. + +Two types of tests are typically run: + +#### Lint tests + +nf-core has a [set of guidelines](https://nf-co.re/docs/specifications/overview) which all pipelines must follow. +To enforce these, run linting with nf-core/tools: + +```bash +nf-core pipelines lint +``` + +If you encounter failures or warnings, follow the linked documentation printed to screen. +For more information about linting tests, see [nf-core/tools API documentation](https://nf-co.re/docs/nf-core-tools/api_reference/latest/pipeline_lint_tests/actions_awsfulltest). + +#### Pipeline tests + +Each nf-core pipeline should be set up with a minimal set of test data. +GitHub Actions runs the pipeline on this data to ensure it runs through and exits successfully. +If there are any failures then the automated tests fail. +These tests are run with the latest available version of Nextflow and the minimum required version specified in the pipeline code. + +### Patch release + +> [!WARNING] +> Only in the unlikely event of a release that contains a critical bug. + +- [ ] Create a new branch `patch` on your fork based on `upstream/main` or `upstream/master`. +- [ ] Fix the bug and use nf-core/tools to bump the version to the next semantic version, for example, `1.2.3` → `1.2.4`. +- [ ] Open a Pull Request from `patch` directly to `main`/`master` with the changes. + +### Pipeline contribution conventions + +nf-core semi-standardises how you write code and other contributions to make the nf-core/phaseimpute code and processing logic more understandable for new contributors and to ensure quality. + +#### Add a new pipeline step + +To contribute a new step to the pipeline, follow the general nf-core coding procedure. +Please also refer to the [pipeline-specific contribution guidelines](#pipeline-specific-contribution-guidelines): + +- [ ] Define the corresponding [input channel](#channel-naming-schemes) into your new process from the expected previous process channel. +- [ ] Install a module with nf-core/tools, or write a local module (see [default processes resource requirements](#default-processes-resource-requirements)), and add it to the target `.nf`. +- [ ] Define the output channel if needed. Mix the version output channel into `ch_versions` and relevant files into `ch_multiqc`. +- [ ] Add new or updated parameters to `nextflow.config` with a [default value](#default-parameter-values). +- [ ] Add new or updated parameters and relevant help text to `nextflow_schema.json` with [nf-core/tools](#default-parameter-values). +- [ ] Add validation for relevant parameters to the pipeline utilisation section of `utils_nfcore_\_pipeline/main.nf` subworkflow. +- [ ] 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. +- [ ] 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. +- [ ] Add a description of the output files and, if relevant, images from the MultiQC report to `docs/output.md`. + +To update the minimum required Nextflow version, see the [Nextflow version bumping](#nextflow-version-bumping) section below. For more information about pipeline contributions, see [pipeline-specific contribution guidelines](#pipeline-specific-contribution-guidelines). + +#### Channel naming schemes + +Use the following naming schemes for channels to make the channel flow easier to understand: + +- Initial process channel: `ch_output_from_` +- Intermediate and terminal channels: `ch__for_` + +#### Default parameter values + +Parameters should be initialised and defined with default values within the `params` scope in `nextflow.config`. +They should also be documented in the pipeline JSON schema. + +To update `nextflow_schema.json`, run: + +```bash +nf-core pipelines schema build +``` + +The schema builder interface that loads in your browser should automatically update the defaults in the parameter documentation. + +#### Default processes resource requirements + +If you write a local module, specify a default set of resource requirements for the process. + +Sensible defaults for process resource requirements (CPUs, memory, time) should be defined in `conf/base.config`. +Specify these with generic `withLabel:` selectors, so they can be shared across multiple processes and steps of the pipeline. + +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)). + +#### Nextflow version bumping + +If you use a new feature from core Nextflow, bump the minimum required Nextflow version in the pipeline with: + +```bash +nf-core pipelines bump-version --nextflow . +``` + +#### Images and figures guidelines + +If you update images or graphics, follow the nf-core [style guidelines](https://nf-co.re/docs/community/brand/workflow-schematics). + +## Pipeline specific contribution guidelines + + diff --git a/docs/usage.md b/docs/usage.md index 6481534d..e944ccd1 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -345,7 +345,7 @@ To facilitate multiple runs of the pipeline with consistent settings without spe Pipeline settings can be provided in a `yaml` or `json` file via `-params-file `. > [!WARNING] -> Do not use `-c ` to specify parameters as this will result in errors. Custom config files specified with `-c` must only be used for [tuning process resource specifications](https://nf-co.re/docs/usage/configuration#tuning-workflow-resources), other infrastructural tweaks (such as output directories), or module arguments (args). +> Do not use `-c ` to specify parameters as this will result in errors. Custom config files specified with `-c` must only be used for [tuning process resource specifications](https://nf-co.re/docs/running/run-pipelines#configuring-pipelines), other infrastructural tweaks (such as output directories), or module arguments (args). The above pipeline run specified with a params file in yaml format: @@ -900,13 +900,13 @@ Specify the path to a specific config file (this is a core Nextflow command). Se Whilst the default requirements set within the pipeline will hopefully work for most people and with most input data, you may find that you want to customise the compute resources that the pipeline requests. Each step in the pipeline has a default set of requirements for number of CPUs, memory and time. For most of the pipeline steps, if the job exits with any of the error codes specified [here](https://github.com/nf-core/rnaseq/blob/4c27ef5610c87db00c3c5a3eed10b1d161abf575/conf/base.config#L18) it will automatically be resubmitted with higher resources request (2 x original, then 3 x original). If it still fails after the third attempt then the pipeline execution is stopped. -To change the resource requests, please see the [max resources](https://nf-co.re/docs/usage/configuration#max-resources) and [tuning workflow resources](https://nf-co.re/docs/usage/configuration#tuning-workflow-resources) section of the nf-core website. +To change the resource requests, please see the [max resources](https://nf-co.re/docs/running/configuration/nextflow-for-your-system#set-max-resources) and [customise process resources](https://nf-co.re/docs/running/configuration/nextflow-for-your-system#customize-process-resources) section of the nf-core website. ### Custom Containers In some cases, you may wish to change the container or conda environment used by a pipeline steps for a particular tool. By default, nf-core pipelines use containers and software from the [biocontainers](https://biocontainers.pro/) or [bioconda](https://bioconda.github.io/) projects. However, in some cases the pipeline specified version maybe out of date. -To use a different container from the default container or conda environment specified in a pipeline, please see the [updating tool versions](https://nf-co.re/docs/usage/configuration#updating-tool-versions) section of the nf-core website. +To use a different container from the default container or conda environment specified in a pipeline, please see the [updating tool versions](https://nf-co.re/docs/running/configuration/nextflow-for-your-system#update-tool-versions) section of the nf-core website. ### Custom Tool Arguments @@ -938,7 +938,7 @@ process { } ``` -To learn how to provide additional arguments to a particular tool of the pipeline, please see the [customising tool arguments](https://nf-co.re/docs/usage/configuration#customising-tool-arguments) section of the nf-core website. +To learn how to provide additional arguments to a particular tool of the pipeline, please see the [customising tool arguments](https://nf-co.re/docs/running/configuration/nextflow-for-your-system#modifying-tool-arguments) section of the nf-core website. ### nf-core/configs diff --git a/main.nf b/main.nf index 19defab3..99ea537d 100644 --- a/main.nf +++ b/main.nf @@ -252,7 +252,6 @@ workflow { params.plaintext_email, params.outdir, params.monochrome_logs, - params.hook_url, NFCORE_PHASEIMPUTE.out.multiqc_report ) } diff --git a/modules.json b/modules.json index bd712cb4..06b37534 100644 --- a/modules.json +++ b/modules.json @@ -153,7 +153,7 @@ }, "multiqc": { "branch": "master", - "git_sha": "79b36b51048048374b642289bfe9e591ef56fe05", + "git_sha": "cd0ad387832473916b1f1c80c2ca673a7883bf94", "installed_by": ["modules"] }, "quilt/quilt": { @@ -272,7 +272,7 @@ }, "utils_nfcore_pipeline": { "branch": "master", - "git_sha": "f0b535b3ae20080f8db03dd5388876ad1ec29d70", + "git_sha": "a3fb7351b1fdb2b1de282b765816bbea190e86a8", "installed_by": ["subworkflows"] }, "utils_nfschema_plugin": { diff --git a/modules/nf-core/multiqc/.conda-lock/linux_amd64-bd-c1f4a7982b743963_1.txt b/modules/nf-core/multiqc/.conda-lock/linux_amd64-bd-839587b417d23042_1.txt similarity index 75% rename from modules/nf-core/multiqc/.conda-lock/linux_amd64-bd-c1f4a7982b743963_1.txt rename to modules/nf-core/multiqc/.conda-lock/linux_amd64-bd-839587b417d23042_1.txt index 76190304..33a1c692 100644 --- a/modules/nf-core/multiqc/.conda-lock/linux_amd64-bd-c1f4a7982b743963_1.txt +++ b/modules/nf-core/multiqc/.conda-lock/linux_amd64-bd-839587b417d23042_1.txt @@ -14,17 +14,17 @@ linux-64: - conda: https://conda.anaconda.org/conda-forge/noarch/_python_abi3_support-1.0-hd8ed1ab_2.conda - conda: https://conda.anaconda.org/conda-forge/noarch/annotated-types-0.7.0-pyhd8ed1ab_1.conda - conda: https://conda.anaconda.org/conda-forge/noarch/attrs-26.1.0-pyhcf101f3_0.conda -- conda: https://conda.anaconda.org/conda-forge/noarch/backports.zstd-1.3.0-py314h680f03e_0.conda +- conda: https://conda.anaconda.org/conda-forge/noarch/backports.zstd-1.5.0-py314h680f03e_0.conda - conda: https://conda.anaconda.org/conda-forge/linux-64/brotli-python-1.2.0-py314h3de4e8d_1.conda - conda: https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-hda65f42_9.conda -- conda: https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2026.2.25-hbd8a1cb_0.conda -- conda: https://conda.anaconda.org/conda-forge/noarch/certifi-2026.2.25-pyhd8ed1ab_0.conda -- conda: https://conda.anaconda.org/conda-forge/noarch/charset-normalizer-3.4.6-pyhd8ed1ab_0.conda -- conda: https://conda.anaconda.org/conda-forge/noarch/click-8.3.1-pyh8f84b5b_1.conda +- conda: https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2026.4.22-hbd8a1cb_0.conda +- conda: https://conda.anaconda.org/conda-forge/noarch/certifi-2026.4.22-pyhd8ed1ab_0.conda +- conda: https://conda.anaconda.org/conda-forge/noarch/charset-normalizer-3.4.7-pyhd8ed1ab_0.conda +- conda: https://conda.anaconda.org/conda-forge/noarch/click-8.4.0-pyhc90fa1f_0.conda - conda: https://conda.anaconda.org/conda-forge/noarch/coloredlogs-15.0.1-pyhd8ed1ab_4.conda - conda: https://conda.anaconda.org/conda-forge/noarch/colormath-3.0.0-pyhd8ed1ab_4.conda -- conda: https://conda.anaconda.org/conda-forge/noarch/cpython-3.14.3-py314hd8ed1ab_101.conda -- conda: https://conda.anaconda.org/conda-forge/linux-64/expat-2.7.4-hecca717_0.conda +- conda: https://conda.anaconda.org/conda-forge/noarch/cpython-3.14.4-py314hd8ed1ab_100.conda +- conda: https://conda.anaconda.org/conda-forge/linux-64/expat-2.8.0-hecca717_0.conda - conda: https://conda.anaconda.org/conda-forge/noarch/font-ttf-dejavu-sans-mono-2.37-hab24e00_0.tar.bz2 - conda: https://conda.anaconda.org/conda-forge/noarch/font-ttf-inconsolata-3.000-h77eed37_0.tar.bz2 - conda: https://conda.anaconda.org/conda-forge/noarch/font-ttf-source-code-pro-2.038-h77eed37_0.tar.bz2 @@ -36,98 +36,95 @@ linux-64: - conda: https://conda.anaconda.org/conda-forge/noarch/humanfriendly-10.0-pyh707e725_8.conda - conda: https://conda.anaconda.org/conda-forge/noarch/humanize-4.15.0-pyhd8ed1ab_0.conda - conda: https://conda.anaconda.org/conda-forge/noarch/hyperframe-6.1.0-pyhd8ed1ab_0.conda -- conda: https://conda.anaconda.org/conda-forge/linux-64/icu-78.3-h33c6efd_0.conda -- conda: https://conda.anaconda.org/conda-forge/noarch/idna-3.11-pyhd8ed1ab_0.conda +- conda: https://conda.anaconda.org/conda-forge/noarch/idna-3.13-pyhcf101f3_0.conda - conda: https://conda.anaconda.org/conda-forge/noarch/importlib-metadata-8.8.0-pyhcf101f3_0.conda - conda: https://conda.anaconda.org/conda-forge/noarch/jinja2-3.1.6-pyhcf101f3_1.conda - conda: https://conda.anaconda.org/conda-forge/noarch/jsonschema-4.26.0-pyhcf101f3_0.conda - conda: https://conda.anaconda.org/conda-forge/noarch/jsonschema-specifications-2025.9.1-pyhcf101f3_0.conda - conda: https://conda.anaconda.org/conda-forge/linux-64/kaleido-core-0.2.1-h3644ca4_0.tar.bz2 -- conda: https://conda.anaconda.org/conda-forge/linux-64/lcms2-2.18-h0c24ade_0.conda +- conda: https://conda.anaconda.org/conda-forge/linux-64/lcms2-2.19.1-h0c24ade_0.conda - conda: https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.45.1-default_hbd61a6d_102.conda - conda: https://conda.anaconda.org/conda-forge/linux-64/lerc-4.1.0-hdb68285_0.conda -- conda: https://conda.anaconda.org/conda-forge/linux-64/libblas-3.11.0-5_h4a7cf45_openblas.conda -- conda: https://conda.anaconda.org/conda-forge/linux-64/libcblas-3.11.0-5_h0358290_openblas.conda +- conda: https://conda.anaconda.org/conda-forge/linux-64/libblas-3.11.0-7_h4a7cf45_openblas.conda +- conda: https://conda.anaconda.org/conda-forge/linux-64/libcblas-3.11.0-7_h0358290_openblas.conda - conda: https://conda.anaconda.org/conda-forge/linux-64/libdeflate-1.25-h17f619e_0.conda -- conda: https://conda.anaconda.org/conda-forge/linux-64/libexpat-2.7.4-hecca717_0.conda +- conda: https://conda.anaconda.org/conda-forge/linux-64/libexpat-2.8.0-hecca717_0.conda - conda: https://conda.anaconda.org/conda-forge/linux-64/libffi-3.5.2-h3435931_0.conda - conda: https://conda.anaconda.org/conda-forge/linux-64/libfreetype-2.14.3-ha770c72_0.conda - conda: https://conda.anaconda.org/conda-forge/linux-64/libfreetype6-2.14.3-h73754d4_0.conda -- conda: https://conda.anaconda.org/conda-forge/linux-64/libgcc-15.2.0-he0feb66_18.conda -- conda: https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-15.2.0-h69a702a_18.conda -- conda: https://conda.anaconda.org/conda-forge/linux-64/libgfortran-15.2.0-h69a702a_18.conda -- conda: https://conda.anaconda.org/conda-forge/linux-64/libgfortran5-15.2.0-h68bc16d_18.conda -- conda: https://conda.anaconda.org/conda-forge/linux-64/libgomp-15.2.0-he0feb66_18.conda -- conda: https://conda.anaconda.org/conda-forge/linux-64/libjpeg-turbo-3.1.2-hb03c661_0.conda -- conda: https://conda.anaconda.org/conda-forge/linux-64/liblapack-3.11.0-5_h47877c9_openblas.conda -- conda: https://conda.anaconda.org/conda-forge/linux-64/liblzma-5.8.2-hb03c661_0.conda +- conda: https://conda.anaconda.org/conda-forge/linux-64/libgcc-15.2.0-he0feb66_19.conda +- conda: https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-15.2.0-h69a702a_19.conda +- conda: https://conda.anaconda.org/conda-forge/linux-64/libgfortran-15.2.0-h69a702a_19.conda +- conda: https://conda.anaconda.org/conda-forge/linux-64/libgfortran5-15.2.0-h68bc16d_19.conda +- conda: https://conda.anaconda.org/conda-forge/linux-64/libgomp-15.2.0-he0feb66_19.conda +- conda: https://conda.anaconda.org/conda-forge/linux-64/libjpeg-turbo-3.1.4.1-hb03c661_0.conda +- conda: https://conda.anaconda.org/conda-forge/linux-64/liblapack-3.11.0-7_h47877c9_openblas.conda +- conda: https://conda.anaconda.org/conda-forge/linux-64/liblzma-5.8.3-hb03c661_0.conda - conda: https://conda.anaconda.org/conda-forge/linux-64/libmpdec-4.0.0-hb03c661_1.conda -- conda: https://conda.anaconda.org/conda-forge/linux-64/libopenblas-0.3.30-pthreads_h94d23a6_4.conda -- conda: https://conda.anaconda.org/conda-forge/linux-64/libpng-1.6.55-h421ea60_0.conda -- conda: https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.52.0-hf4e2dac_0.conda -- conda: https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-15.2.0-h934c35e_18.conda +- conda: https://conda.anaconda.org/conda-forge/linux-64/libopenblas-0.3.33-pthreads_h94d23a6_0.conda +- conda: https://conda.anaconda.org/conda-forge/linux-64/libpng-1.6.58-h421ea60_0.conda +- conda: https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.53.1-h0c1763c_0.conda +- conda: https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-15.2.0-h934c35e_19.conda - conda: https://conda.anaconda.org/conda-forge/linux-64/libtiff-4.7.1-h9d88235_1.conda -- conda: https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.41.3-h5347b49_0.conda +- conda: https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.42.1-h5347b49_0.conda - conda: https://conda.anaconda.org/conda-forge/linux-64/libwebp-base-1.6.0-hd42ef1d_0.conda - conda: https://conda.anaconda.org/conda-forge/linux-64/libxcb-1.17.0-h8a09558_0.conda - conda: https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.3.2-h25fd6f3_2.conda - conda: https://conda.anaconda.org/conda-forge/noarch/markdown-3.10.2-pyhcf101f3_0.conda -- conda: https://conda.anaconda.org/conda-forge/noarch/markdown-it-py-4.0.0-pyhd8ed1ab_0.conda +- conda: https://conda.anaconda.org/conda-forge/noarch/markdown-it-py-4.2.0-pyhd8ed1ab_0.conda - conda: https://conda.anaconda.org/conda-forge/linux-64/markupsafe-3.0.3-py314h67df5f8_1.conda - conda: https://conda.anaconda.org/conda-forge/linux-64/mathjax-2.7.7-ha770c72_3.tar.bz2 - conda: https://conda.anaconda.org/conda-forge/noarch/mdurl-0.1.2-pyhd8ed1ab_1.conda -- conda: https://conda.anaconda.org/bioconda/noarch/multiqc-1.33-pyhdfd78af_0.conda -- conda: https://conda.anaconda.org/conda-forge/noarch/narwhals-2.18.1-pyhcf101f3_1.conda +- conda: https://conda.anaconda.org/bioconda/noarch/multiqc-1.35-pyhdfd78af_0.conda +- conda: https://conda.anaconda.org/conda-forge/noarch/narwhals-2.21.2-pyhcf101f3_0.conda - conda: https://conda.anaconda.org/conda-forge/noarch/natsort-8.4.0-pyhcf101f3_2.conda -- conda: https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h2d0b736_3.conda +- conda: https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.6-hdb14827_0.conda - conda: https://conda.anaconda.org/conda-forge/noarch/networkx-3.6.1-pyhcf101f3_0.conda - conda: https://conda.anaconda.org/conda-forge/linux-64/nspr-4.38-h29cc59b_0.conda - conda: https://conda.anaconda.org/conda-forge/linux-64/nss-3.118-h445c969_0.conda -- conda: https://conda.anaconda.org/conda-forge/linux-64/numpy-2.4.3-py314h2b28147_0.conda +- conda: https://conda.anaconda.org/conda-forge/linux-64/numpy-2.4.5-py314h2b28147_0.conda - conda: https://conda.anaconda.org/conda-forge/linux-64/openjpeg-2.5.4-h55fea9a_0.conda -- conda: https://conda.anaconda.org/conda-forge/linux-64/openssl-3.6.1-h35e630c_1.conda -- conda: https://conda.anaconda.org/conda-forge/noarch/packaging-26.0-pyhcf101f3_0.conda -- conda: https://conda.anaconda.org/conda-forge/linux-64/pillow-12.1.1-py314h8ec4b1a_0.conda +- conda: https://conda.anaconda.org/conda-forge/linux-64/openssl-3.6.2-h35e630c_0.conda +- conda: https://conda.anaconda.org/conda-forge/noarch/packaging-26.2-pyhc364b38_0.conda +- conda: https://conda.anaconda.org/conda-forge/linux-64/pillow-12.2.0-py314h8ec4b1a_0.conda - conda: https://conda.anaconda.org/conda-forge/noarch/plotly-6.6.0-pyhd8ed1ab_0.conda -- conda: https://conda.anaconda.org/conda-forge/noarch/polars-1.39.3-pyh58ad624_1.conda -- conda: https://conda.anaconda.org/conda-forge/noarch/polars-lts-cpu-1.34.0.deprecated-hc364b38_0.conda -- conda: https://conda.anaconda.org/conda-forge/linux-64/polars-runtime-32-1.39.3-py310hffdcd12_1.conda -- conda: https://conda.anaconda.org/conda-forge/linux-64/polars-runtime-compat-1.39.3-py310hbcd5346_1.conda +- conda: https://conda.anaconda.org/conda-forge/noarch/polars-1.40.1-pyh58ad624_1.conda +- conda: https://conda.anaconda.org/conda-forge/linux-64/polars-runtime-32-1.40.1-py310h49dadd8_1.conda - conda: https://conda.anaconda.org/conda-forge/linux-64/procps-ng-4.0.6-h18c060e_0.conda - conda: https://conda.anaconda.org/conda-forge/linux-64/pthread-stubs-0.4-hb9d3cd8_1002.conda - conda: https://conda.anaconda.org/conda-forge/noarch/pyaml-env-1.2.2-pyhd8ed1ab_0.conda -- conda: https://conda.anaconda.org/conda-forge/noarch/pydantic-2.12.5-pyhcf101f3_1.conda -- conda: https://conda.anaconda.org/conda-forge/linux-64/pydantic-core-2.41.5-py314h2e6c369_1.conda -- conda: https://conda.anaconda.org/conda-forge/noarch/pygments-2.19.2-pyhd8ed1ab_0.conda +- conda: https://conda.anaconda.org/conda-forge/noarch/pydantic-2.13.4-pyhcf101f3_0.conda +- conda: https://conda.anaconda.org/conda-forge/linux-64/pydantic-core-2.46.4-py314h2e6c369_0.conda +- conda: https://conda.anaconda.org/conda-forge/noarch/pygments-2.20.0-pyhd8ed1ab_0.conda - conda: https://conda.anaconda.org/conda-forge/noarch/pysocks-1.7.1-pyha55dd90_7.conda -- conda: https://conda.anaconda.org/conda-forge/linux-64/python-3.14.3-h32b2ec7_101_cp314.conda +- conda: https://conda.anaconda.org/conda-forge/linux-64/python-3.14.4-habeac84_100_cp314.conda - conda: https://conda.anaconda.org/conda-forge/noarch/python-dotenv-1.2.2-pyhcf101f3_0.conda -- conda: https://conda.anaconda.org/conda-forge/noarch/python-gil-3.14.3-h4df99d1_101.conda +- conda: https://conda.anaconda.org/conda-forge/noarch/python-gil-3.14.4-h4df99d1_100.conda - conda: https://conda.anaconda.org/conda-forge/noarch/python-kaleido-0.2.1-pyhd8ed1ab_0.tar.bz2 - conda: https://conda.anaconda.org/conda-forge/noarch/python_abi-3.14-8_cp314.conda - conda: https://conda.anaconda.org/conda-forge/linux-64/pyyaml-6.0.3-py314h67df5f8_1.conda - conda: https://conda.anaconda.org/conda-forge/linux-64/readline-8.3-h853b02a_0.conda - conda: https://conda.anaconda.org/conda-forge/noarch/referencing-0.37.0-pyhcf101f3_0.conda -- conda: https://conda.anaconda.org/conda-forge/linux-64/regex-2026.2.28-py314h5bd0f2a_0.conda -- conda: https://conda.anaconda.org/conda-forge/noarch/requests-2.32.5-pyhcf101f3_1.conda -- conda: https://conda.anaconda.org/conda-forge/noarch/rich-14.3.3-pyhcf101f3_0.conda +- conda: https://conda.anaconda.org/conda-forge/linux-64/regex-2026.5.9-py314h5bd0f2a_0.conda +- conda: https://conda.anaconda.org/conda-forge/noarch/requests-2.34.2-pyhcf101f3_0.conda +- conda: https://conda.anaconda.org/conda-forge/noarch/rich-15.0.0-pyhcf101f3_0.conda - conda: https://conda.anaconda.org/conda-forge/noarch/rich-click-1.9.7-pyh8f84b5b_0.conda - conda: https://conda.anaconda.org/conda-forge/linux-64/rpds-py-0.30.0-py314h2e6c369_0.conda - conda: https://conda.anaconda.org/conda-forge/noarch/spectra-0.0.11-pyhd8ed1ab_2.conda -- conda: https://conda.anaconda.org/conda-forge/linux-64/sqlite-3.52.0-h04a0ce9_0.conda +- conda: https://conda.anaconda.org/conda-forge/linux-64/sqlite-3.53.1-hbc0de68_0.conda - conda: https://conda.anaconda.org/conda-forge/linux-64/tiktoken-0.12.0-py314h67fec18_3.conda - conda: https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.13-noxft_h366c992_103.conda - conda: https://conda.anaconda.org/conda-forge/noarch/tqdm-4.67.3-pyh8f84b5b_0.conda -- conda: https://conda.anaconda.org/conda-forge/noarch/typeguard-4.5.1-pyhd8ed1ab_0.conda +- conda: https://conda.anaconda.org/conda-forge/noarch/typeguard-4.5.2-pyhcf101f3_0.conda - conda: https://conda.anaconda.org/conda-forge/noarch/typing-extensions-4.15.0-h396c80c_0.conda -- conda: https://conda.anaconda.org/conda-forge/noarch/typing-inspection-0.4.2-pyhd8ed1ab_1.conda +- conda: https://conda.anaconda.org/conda-forge/noarch/typing-inspection-0.4.2-pyhcf101f3_2.conda - conda: https://conda.anaconda.org/conda-forge/noarch/typing_extensions-4.15.0-pyhcf101f3_0.conda - conda: https://conda.anaconda.org/conda-forge/noarch/tzdata-2025c-hc9c84f9_1.conda -- conda: https://conda.anaconda.org/conda-forge/noarch/urllib3-2.6.3-pyhd8ed1ab_0.conda +- conda: https://conda.anaconda.org/conda-forge/noarch/urllib3-2.7.0-pyhd8ed1ab_0.conda - conda: https://conda.anaconda.org/conda-forge/linux-64/xorg-libxau-1.0.12-hb03c661_1.conda - conda: https://conda.anaconda.org/conda-forge/linux-64/xorg-libxdmcp-1.1.5-hb03c661_1.conda - conda: https://conda.anaconda.org/conda-forge/linux-64/yaml-0.2.5-h280c20c_3.conda -- conda: https://conda.anaconda.org/conda-forge/noarch/zipp-3.23.0-pyhcf101f3_1.conda +- conda: https://conda.anaconda.org/conda-forge/noarch/zipp-4.1.0-pyhcf101f3_0.conda - conda: https://conda.anaconda.org/conda-forge/linux-64/zlib-ng-2.3.3-hceb46e0_1.conda - conda: https://conda.anaconda.org/conda-forge/linux-64/zstd-1.5.7-hb78ec9c_6.conda packages: @@ -174,15 +171,15 @@ license: MIT license_family: MIT size: 64927 timestamp: 1773935801332 -- conda: https://conda.anaconda.org/conda-forge/noarch/backports.zstd-1.3.0-py314h680f03e_0.conda +- conda: https://conda.anaconda.org/conda-forge/noarch/backports.zstd-1.5.0-py314h680f03e_0.conda noarch: generic -sha256: c31ab719d256bc6f89926131e88ecd0f0c5d003fe8481852c6424f4ec6c7eb29 -md5: a2ac7763a9ac75055b68f325d3255265 +sha256: a1c97297e867776760489537bc5ae36fa83a154be30e3b79385a39ca4cb058fe +md5: 1133126d840e75287d83947be3fc3e71 depends: - python >=3.14 license: BSD-3-Clause AND MIT AND EPL-2.0 -size: 7514 -timestamp: 1767044983590 +size: 7533 +timestamp: 1778594057496 - conda: https://conda.anaconda.org/conda-forge/linux-64/brotli-python-1.2.0-py314h3de4e8d_1.conda sha256: 3ad3500bff54a781c29f16ce1b288b36606e2189d0b0ef2f67036554f47f12b0 md5: 8910d2c46f7e7b519129f486e0fe927a @@ -208,42 +205,41 @@ license: bzip2-1.0.6 license_family: BSD size: 260182 timestamp: 1771350215188 -- conda: https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2026.2.25-hbd8a1cb_0.conda -sha256: 67cc7101b36421c5913a1687ef1b99f85b5d6868da3abbf6ec1a4181e79782fc -md5: 4492fd26db29495f0ba23f146cd5638d +- conda: https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2026.4.22-hbd8a1cb_0.conda +sha256: c9dbcc8039a52023660d6d1bbf87594a93dd69c6ac5a2a44323af2c92976728d +md5: e18ad67cf881dcadee8b8d9e2f8e5f73 depends: - __unix license: ISC -size: 147413 -timestamp: 1772006283803 -- conda: https://conda.anaconda.org/conda-forge/noarch/certifi-2026.2.25-pyhd8ed1ab_0.conda -sha256: a6b118fd1ed6099dc4fc03f9c492b88882a780fadaef4ed4f93dc70757713656 -md5: 765c4d97e877cdbbb88ff33152b86125 +size: 131039 +timestamp: 1776865545798 +- conda: https://conda.anaconda.org/conda-forge/noarch/certifi-2026.4.22-pyhd8ed1ab_0.conda +sha256: 989db6e5957c4b44fa600c68c681ec2f36a55e48f7c7f1c073d5e91caa8cd878 +md5: 929471569c93acefb30282a22060dcd5 depends: - python >=3.10 license: ISC -size: 151445 -timestamp: 1772001170301 -- conda: https://conda.anaconda.org/conda-forge/noarch/charset-normalizer-3.4.6-pyhd8ed1ab_0.conda -sha256: d86dfd428b2e3c364fa90e07437c8405d635aa4ef54b25ab51d9c712be4112a5 -md5: 49ee13eb9b8f44d63879c69b8a40a74b +size: 135656 +timestamp: 1776866680878 +- conda: https://conda.anaconda.org/conda-forge/noarch/charset-normalizer-3.4.7-pyhd8ed1ab_0.conda +sha256: 3f9483d62ce24ecd063f8a5a714448445dc8d9e201147c46699fc0033e824457 +md5: a9167b9571f3baa9d448faa2139d1089 depends: - python >=3.10 license: MIT license_family: MIT -size: 58510 -timestamp: 1773660086450 -- conda: https://conda.anaconda.org/conda-forge/noarch/click-8.3.1-pyh8f84b5b_1.conda -sha256: 38cfe1ee75b21a8361c8824f5544c3866f303af1762693a178266d7f198e8715 -md5: ea8a6c3256897cc31263de9f455e25d9 +size: 58872 +timestamp: 1775127203018 +- conda: https://conda.anaconda.org/conda-forge/noarch/click-8.4.0-pyhc90fa1f_0.conda +sha256: 99ab8ef815c4520cce3a7482c2513f377c14348206857661d84c76a55e030f97 +md5: 003767c47f1f0a474c4de268b57839c3 depends: -- python >=3.10 - __unix - python +- python >=3.10 license: BSD-3-Clause -license_family: BSD -size: 97676 -timestamp: 1764518652276 +size: 104631 +timestamp: 1779108494556 - conda: https://conda.anaconda.org/conda-forge/noarch/coloredlogs-15.0.1-pyhd8ed1ab_4.conda sha256: 8021c76eeadbdd5784b881b165242db9449783e12ce26d6234060026fd6a8680 md5: b866ff7007b934d564961066c8195983 @@ -265,27 +261,27 @@ license: BSD-3-Clause license_family: BSD size: 39326 timestamp: 1735759976140 -- conda: https://conda.anaconda.org/conda-forge/noarch/cpython-3.14.3-py314hd8ed1ab_101.conda +- conda: https://conda.anaconda.org/conda-forge/noarch/cpython-3.14.4-py314hd8ed1ab_100.conda noarch: generic -sha256: 91b06300879df746214f7363d6c27c2489c80732e46a369eb2afc234bcafb44c -md5: 3bb89e4f795e5414addaa531d6b1500a +sha256: 40dc224f2b718e5f034efd2332bc315a719063235f63673468d26a24770094ee +md5: f111d4cfaf1fe9496f386bc98ae94452 depends: - python >=3.14,<3.15.0a0 - python_abi * *_cp314 license: Python-2.0 -size: 50078 -timestamp: 1770674447292 -- conda: https://conda.anaconda.org/conda-forge/linux-64/expat-2.7.4-hecca717_0.conda -sha256: 0cc345e4dead417996ce9a1f088b28d858f03d113d43c1963d29194366dcce27 -md5: a0535741a4934b3e386051065c58761a +size: 49809 +timestamp: 1775614256655 +- conda: https://conda.anaconda.org/conda-forge/linux-64/expat-2.8.0-hecca717_0.conda +sha256: ca4dc1da00a8aaa56c1088e7f45f1859ecea6f75874e67584f1af6e5cf8179f8 +md5: 992e529e407c9d67d50be1d7543fde4c depends: - __glibc >=2.17,<3.0.a0 -- libexpat 2.7.4 hecca717_0 +- libexpat 2.8.0 hecca717_0 - libgcc >=14 license: MIT license_family: MIT -size: 145274 -timestamp: 1771259434699 +size: 148114 +timestamp: 1777846120303 - conda: https://conda.anaconda.org/conda-forge/noarch/font-ttf-dejavu-sans-mono-2.37-hab24e00_0.tar.bz2 sha256: 58d7f40d2940dd0a8aa28651239adbf5613254df0f75789919c4e6762054403b md5: 0c96522c6bdaed4b1566d11387caaf45 @@ -390,26 +386,16 @@ license: MIT license_family: MIT size: 17397 timestamp: 1737618427549 -- conda: https://conda.anaconda.org/conda-forge/linux-64/icu-78.3-h33c6efd_0.conda -sha256: fbf86c4a59c2ed05bbffb2ba25c7ed94f6185ec30ecb691615d42342baa1a16a -md5: c80d8a3b84358cb967fa81e7075fbc8a -depends: -- __glibc >=2.17,<3.0.a0 -- libgcc >=14 -- libstdcxx >=14 -license: MIT -license_family: MIT -size: 12723451 -timestamp: 1773822285671 -- conda: https://conda.anaconda.org/conda-forge/noarch/idna-3.11-pyhd8ed1ab_0.conda -sha256: ae89d0299ada2a3162c2614a9d26557a92aa6a77120ce142f8e0109bbf0342b0 -md5: 53abe63df7e10a6ba605dc5f9f961d36 +- conda: https://conda.anaconda.org/conda-forge/noarch/idna-3.13-pyhcf101f3_0.conda +sha256: 9ab620e6f64bb67737bd7bc1ad6f480770124e304c6710617aba7fe60b089f48 +md5: fb7130c190f9b4ec91219840a05ba3ac depends: - python >=3.10 +- python license: BSD-3-Clause license_family: BSD -size: 50721 -timestamp: 1760286526795 +size: 59038 +timestamp: 1776947141407 - conda: https://conda.anaconda.org/conda-forge/noarch/importlib-metadata-8.8.0-pyhcf101f3_0.conda sha256: 82ab2a0d91ca1e7e63ab6a4939356667ef683905dea631bc2121aa534d347b16 md5: 080594bf4493e6bae2607e65390c520a @@ -474,18 +460,18 @@ license: MIT license_family: MIT size: 62099926 timestamp: 1615199463039 -- conda: https://conda.anaconda.org/conda-forge/linux-64/lcms2-2.18-h0c24ade_0.conda -sha256: 836ec4b895352110335b9fdcfa83a8dcdbe6c5fb7c06c4929130600caea91c0a -md5: 6f2e2c8f58160147c4d1c6f4c14cbac4 +- conda: https://conda.anaconda.org/conda-forge/linux-64/lcms2-2.19.1-h0c24ade_0.conda +sha256: eb89c6c39f2f6a93db55723dbb2f6bba8c8e63e6312bf1abf13e6e9ff45849c8 +md5: f92f984b558e6e6204014b16d212b271 depends: - __glibc >=2.17,<3.0.a0 - libgcc >=14 -- libjpeg-turbo >=3.1.2,<4.0a0 +- libjpeg-turbo >=3.1.4.1,<4.0a0 - libtiff >=4.7.1,<4.8.0a0 license: MIT license_family: MIT -size: 249959 -timestamp: 1768184673131 +size: 251086 +timestamp: 1778079286384 - conda: https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.45.1-default_hbd61a6d_102.conda sha256: 3d584956604909ff5df353767f3a2a2f60e07d070b328d109f30ac40cd62df6c md5: 18335a698559cdbcd86150a48bf54ba6 @@ -509,37 +495,37 @@ license: Apache-2.0 license_family: Apache size: 261513 timestamp: 1773113328888 -- conda: https://conda.anaconda.org/conda-forge/linux-64/libblas-3.11.0-5_h4a7cf45_openblas.conda -build_number: 5 -sha256: 18c72545080b86739352482ba14ba2c4815e19e26a7417ca21a95b76ec8da24c -md5: c160954f7418d7b6e87eaf05a8913fa9 +- conda: https://conda.anaconda.org/conda-forge/linux-64/libblas-3.11.0-7_h4a7cf45_openblas.conda +build_number: 7 +sha256: 081c850f99bc355821fac9c6e3727d40b3f8ce3beb50a5437cf03726b611ff39 +md5: 955b44e8b00b7f7ef4ce0130cef12394 depends: -- libopenblas >=0.3.30,<0.3.31.0a0 -- libopenblas >=0.3.30,<1.0a0 +- libopenblas >=0.3.33,<0.3.34.0a0 +- libopenblas >=0.3.33,<1.0a0 constrains: -- mkl <2026 -- liblapack 3.11.0 5*_openblas -- libcblas 3.11.0 5*_openblas -- blas 2.305 openblas -- liblapacke 3.11.0 5*_openblas +- libcblas 3.11.0 7*_openblas +- blas 2.307 openblas +- liblapack 3.11.0 7*_openblas +- liblapacke 3.11.0 7*_openblas +- mkl <2027 license: BSD-3-Clause license_family: BSD -size: 18213 -timestamp: 1765818813880 -- conda: https://conda.anaconda.org/conda-forge/linux-64/libcblas-3.11.0-5_h0358290_openblas.conda -build_number: 5 -sha256: 0cbdcc67901e02dc17f1d19e1f9170610bd828100dc207de4d5b6b8ad1ae7ad8 -md5: 6636a2b6f1a87572df2970d3ebc87cc0 -depends: -- libblas 3.11.0 5_h4a7cf45_openblas +size: 18716 +timestamp: 1778489854108 +- conda: https://conda.anaconda.org/conda-forge/linux-64/libcblas-3.11.0-7_h0358290_openblas.conda +build_number: 7 +sha256: 956ae0bb1ec8b0c3663d75b151aceb0521b54e513bf97f621a035f9c87037970 +md5: 0675639dc24cb0032f199e7ff68e4633 +depends: +- libblas 3.11.0 7_h4a7cf45_openblas constrains: -- liblapacke 3.11.0 5*_openblas -- blas 2.305 openblas -- liblapack 3.11.0 5*_openblas +- liblapacke 3.11.0 7*_openblas +- blas 2.307 openblas +- liblapack 3.11.0 7*_openblas license: BSD-3-Clause license_family: BSD -size: 18194 -timestamp: 1765818837135 +size: 18675 +timestamp: 1778489861559 - conda: https://conda.anaconda.org/conda-forge/linux-64/libdeflate-1.25-h17f619e_0.conda sha256: aa8e8c4be9a2e81610ddf574e05b64ee131fab5e0e3693210c9d6d2fba32c680 md5: 6c77a605a7a689d17d4819c0f8ac9a00 @@ -550,18 +536,18 @@ license: MIT license_family: MIT size: 73490 timestamp: 1761979956660 -- conda: https://conda.anaconda.org/conda-forge/linux-64/libexpat-2.7.4-hecca717_0.conda -sha256: d78f1d3bea8c031d2f032b760f36676d87929b18146351c4464c66b0869df3f5 -md5: e7f7ce06ec24cfcfb9e36d28cf82ba57 +- conda: https://conda.anaconda.org/conda-forge/linux-64/libexpat-2.8.0-hecca717_0.conda +sha256: ea33c40977ea7a2c3658c522230058395bc2ee0d89d99f0711390b6a1ee80d12 +md5: a3b390520c563d78cc58974de95a03e5 depends: - __glibc >=2.17,<3.0.a0 - libgcc >=14 constrains: -- expat 2.7.4.* +- expat 2.8.0.* license: MIT license_family: MIT -size: 76798 -timestamp: 1771259418166 +size: 77241 +timestamp: 1777846112704 - conda: https://conda.anaconda.org/conda-forge/linux-64/libffi-3.5.2-h3435931_0.conda sha256: 31f19b6a88ce40ebc0d5a992c131f57d919f73c0b92cd1617a5bec83f6e961e6 md5: a360c33a5abe61c07959e449fa1453eb @@ -593,42 +579,42 @@ constrains: license: GPL-2.0-only OR FTL size: 384575 timestamp: 1774298162622 -- conda: https://conda.anaconda.org/conda-forge/linux-64/libgcc-15.2.0-he0feb66_18.conda -sha256: faf7d2017b4d718951e3a59d081eb09759152f93038479b768e3d612688f83f5 -md5: 0aa00f03f9e39fb9876085dee11a85d4 +- conda: https://conda.anaconda.org/conda-forge/linux-64/libgcc-15.2.0-he0feb66_19.conda +sha256: 8e0a3b5e41272e5678499b5dfc4cddb673f9e935de01eb0767ce857001229f46 +md5: 57736f29cc2b0ec0b6c2952d3f101b6a depends: - __glibc >=2.17,<3.0.a0 - _openmp_mutex >=4.5 constrains: -- libgcc-ng ==15.2.0=*_18 -- libgomp 15.2.0 he0feb66_18 +- libgcc-ng ==15.2.0=*_19 +- libgomp 15.2.0 he0feb66_19 license: GPL-3.0-only WITH GCC-exception-3.1 license_family: GPL -size: 1041788 -timestamp: 1771378212382 -- conda: https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-15.2.0-h69a702a_18.conda -sha256: e318a711400f536c81123e753d4c797a821021fb38970cebfb3f454126016893 -md5: d5e96b1ed75ca01906b3d2469b4ce493 +size: 1041084 +timestamp: 1778269013026 +- conda: https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-15.2.0-h69a702a_19.conda +sha256: 9dcf54adfaa5e861123c2da4f2f0451a685464ea7e5a41ad91cf67b31d658d98 +md5: 331ee9b72b9dff570d56b1302c5ab37d depends: -- libgcc 15.2.0 he0feb66_18 +- libgcc 15.2.0 he0feb66_19 license: GPL-3.0-only WITH GCC-exception-3.1 license_family: GPL -size: 27526 -timestamp: 1771378224552 -- conda: https://conda.anaconda.org/conda-forge/linux-64/libgfortran-15.2.0-h69a702a_18.conda -sha256: d2c9fad338fd85e4487424865da8e74006ab2e2475bd788f624d7a39b2a72aee -md5: 9063115da5bc35fdc3e1002e69b9ef6e +size: 27694 +timestamp: 1778269016987 +- conda: https://conda.anaconda.org/conda-forge/linux-64/libgfortran-15.2.0-h69a702a_19.conda +sha256: 561a42758ef25b9ce308c4e2cf56daee4f06138385a17e29a492cd928e00be6f +md5: 42bf7eca1a951735fa06c0e3c0d5c8e6 depends: -- libgfortran5 15.2.0 h68bc16d_18 +- libgfortran5 15.2.0 h68bc16d_19 constrains: -- libgfortran-ng ==15.2.0=*_18 +- libgfortran-ng ==15.2.0=*_19 license: GPL-3.0-only WITH GCC-exception-3.1 license_family: GPL -size: 27523 -timestamp: 1771378269450 -- conda: https://conda.anaconda.org/conda-forge/linux-64/libgfortran5-15.2.0-h68bc16d_18.conda -sha256: 539b57cf50ec85509a94ba9949b7e30717839e4d694bc94f30d41c9d34de2d12 -md5: 646855f357199a12f02a87382d429b75 +size: 27655 +timestamp: 1778269042954 +- conda: https://conda.anaconda.org/conda-forge/linux-64/libgfortran5-15.2.0-h68bc16d_19.conda +sha256: 057978bb69fea29ed715a9b98adf71015c31baecc4aeb2bfc20d4fd5d83579d4 +md5: 85072b0ad177c966294f129b7c04a2d5 depends: - __glibc >=2.17,<3.0.a0 - libgcc >=15.2.0 @@ -636,53 +622,53 @@ constrains: - libgfortran 15.2.0 license: GPL-3.0-only WITH GCC-exception-3.1 license_family: GPL -size: 2482475 -timestamp: 1771378241063 -- conda: https://conda.anaconda.org/conda-forge/linux-64/libgomp-15.2.0-he0feb66_18.conda -sha256: 21337ab58e5e0649d869ab168d4e609b033509de22521de1bfed0c031bfc5110 -md5: 239c5e9546c38a1e884d69effcf4c882 +size: 2483673 +timestamp: 1778269025089 +- conda: https://conda.anaconda.org/conda-forge/linux-64/libgomp-15.2.0-he0feb66_19.conda +sha256: 5abe4ab9d93f6c9757d654f1969ae2267d4505315c1f2f8fe705fd60af084f1b +md5: faac990cb7aedc7f3a2224f2c9b0c26c depends: - __glibc >=2.17,<3.0.a0 license: GPL-3.0-only WITH GCC-exception-3.1 license_family: GPL -size: 603262 -timestamp: 1771378117851 -- conda: https://conda.anaconda.org/conda-forge/linux-64/libjpeg-turbo-3.1.2-hb03c661_0.conda -sha256: cc9aba923eea0af8e30e0f94f2ad7156e2984d80d1e8e7fe6be5a1f257f0eb32 -md5: 8397539e3a0bbd1695584fb4f927485a +size: 603817 +timestamp: 1778268942614 +- conda: https://conda.anaconda.org/conda-forge/linux-64/libjpeg-turbo-3.1.4.1-hb03c661_0.conda +sha256: 10056646c28115b174de81a44e23e3a0a3b95b5347d2e6c45cc6d49d35294256 +md5: 6178c6f2fb254558238ef4e6c56fb782 depends: - __glibc >=2.17,<3.0.a0 - libgcc >=14 constrains: - jpeg <0.0.0a license: IJG AND BSD-3-Clause AND Zlib -size: 633710 -timestamp: 1762094827865 -- conda: https://conda.anaconda.org/conda-forge/linux-64/liblapack-3.11.0-5_h47877c9_openblas.conda -build_number: 5 -sha256: c723b6599fcd4c6c75dee728359ef418307280fa3e2ee376e14e85e5bbdda053 -md5: b38076eb5c8e40d0106beda6f95d7609 -depends: -- libblas 3.11.0 5_h4a7cf45_openblas +size: 633831 +timestamp: 1775962768273 +- conda: https://conda.anaconda.org/conda-forge/linux-64/liblapack-3.11.0-7_h47877c9_openblas.conda +build_number: 7 +sha256: 96962084921f197c9ad13fb7f8b324f2351d50ff3d8d962148751ad532f54a01 +md5: 6569b4f273740e25dc0dc7e3232c2a6c +depends: +- libblas 3.11.0 7_h4a7cf45_openblas constrains: -- blas 2.305 openblas -- liblapacke 3.11.0 5*_openblas -- libcblas 3.11.0 5*_openblas +- liblapacke 3.11.0 7*_openblas +- libcblas 3.11.0 7*_openblas +- blas 2.307 openblas license: BSD-3-Clause license_family: BSD -size: 18200 -timestamp: 1765818857876 -- conda: https://conda.anaconda.org/conda-forge/linux-64/liblzma-5.8.2-hb03c661_0.conda -sha256: 755c55ebab181d678c12e49cced893598f2bab22d582fbbf4d8b83c18be207eb -md5: c7c83eecbb72d88b940c249af56c8b17 +size: 18694 +timestamp: 1778489869038 +- conda: https://conda.anaconda.org/conda-forge/linux-64/liblzma-5.8.3-hb03c661_0.conda +sha256: ec30e52a3c1bf7d0425380a189d209a52baa03f22fb66dd3eb587acaa765bd6d +md5: b88d90cad08e6bc8ad540cb310a761fb depends: - __glibc >=2.17,<3.0.a0 - libgcc >=14 constrains: -- xz 5.8.2.* +- xz 5.8.3.* license: 0BSD -size: 113207 -timestamp: 1768752626120 +size: 113478 +timestamp: 1775825492909 - conda: https://conda.anaconda.org/conda-forge/linux-64/libmpdec-4.0.0-hb03c661_1.conda sha256: fe171ed5cf5959993d43ff72de7596e8ac2853e9021dec0344e583734f1e0843 md5: 2c21e66f50753a083cbe6b80f38268fa @@ -693,53 +679,52 @@ license: BSD-2-Clause license_family: BSD size: 92400 timestamp: 1769482286018 -- conda: https://conda.anaconda.org/conda-forge/linux-64/libopenblas-0.3.30-pthreads_h94d23a6_4.conda -sha256: 199d79c237afb0d4780ccd2fbf829cea80743df60df4705202558675e07dd2c5 -md5: be43915efc66345cccb3c310b6ed0374 +- conda: https://conda.anaconda.org/conda-forge/linux-64/libopenblas-0.3.33-pthreads_h94d23a6_0.conda +sha256: 3d9aa85648e5e18a6d66db98b8c4317cc426721ad7a220aa86330d1ccedc8903 +md5: 2d3278b721e40468295ca755c3b84070 depends: - __glibc >=2.17,<3.0.a0 - libgcc >=14 - libgfortran - libgfortran5 >=14.3.0 constrains: -- openblas >=0.3.30,<0.3.31.0a0 +- openblas >=0.3.33,<0.3.34.0a0 license: BSD-3-Clause license_family: BSD -size: 5927939 -timestamp: 1763114673331 -- conda: https://conda.anaconda.org/conda-forge/linux-64/libpng-1.6.55-h421ea60_0.conda -sha256: 36ade759122cdf0f16e2a2562a19746d96cf9c863ffaa812f2f5071ebbe9c03c -md5: 5f13ffc7d30ffec87864e678df9957b4 +size: 5931919 +timestamp: 1776993658641 +- conda: https://conda.anaconda.org/conda-forge/linux-64/libpng-1.6.58-h421ea60_0.conda +sha256: 377cfe037f3eeb3b1bf3ad333f724a64d32f315ee1958581fc671891d63d3f89 +md5: eba48a68a1a2b9d3c0d9511548db85db depends: -- libgcc >=14 - __glibc >=2.17,<3.0.a0 -- libzlib >=1.3.1,<2.0a0 +- libgcc >=14 +- libzlib >=1.3.2,<2.0a0 license: zlib-acknowledgement -size: 317669 -timestamp: 1770691470744 -- conda: https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.52.0-hf4e2dac_0.conda -sha256: d716847b7deca293d2e49ed1c8ab9e4b9e04b9d780aea49a97c26925b28a7993 -md5: fd893f6a3002a635b5e50ceb9dd2c0f4 +size: 317729 +timestamp: 1776315175087 +- conda: https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.53.1-h0c1763c_0.conda +sha256: 54cdcd3214313b62c2a8ee277e6f42150d9b748264c1b70d958bf735e420ef8d +md5: 7dc38adcbf71e6b38748e919e16e0dce depends: - __glibc >=2.17,<3.0.a0 -- icu >=78.2,<79.0a0 - libgcc >=14 -- libzlib >=1.3.1,<2.0a0 +- libzlib >=1.3.2,<2.0a0 license: blessing -size: 951405 -timestamp: 1772818874251 -- conda: https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-15.2.0-h934c35e_18.conda -sha256: 78668020064fdaa27e9ab65cd2997e2c837b564ab26ce3bf0e58a2ce1a525c6e -md5: 1b08cd684f34175e4514474793d44bcb +size: 954962 +timestamp: 1777986471789 +- conda: https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-15.2.0-h934c35e_19.conda +sha256: dff1058c76ec6b8759e41cefa2508162d00e4a5e6721aa68ec3fd10094e702dc +md5: 5794b3bdc38177caf969dabd3af08549 depends: - __glibc >=2.17,<3.0.a0 -- libgcc 15.2.0 he0feb66_18 +- libgcc 15.2.0 he0feb66_19 constrains: -- libstdcxx-ng ==15.2.0=*_18 +- libstdcxx-ng ==15.2.0=*_19 license: GPL-3.0-only WITH GCC-exception-3.1 license_family: GPL -size: 5852330 -timestamp: 1771378262446 +size: 5852044 +timestamp: 1778269036376 - conda: https://conda.anaconda.org/conda-forge/linux-64/libtiff-4.7.1-h9d88235_1.conda sha256: e5f8c38625aa6d567809733ae04bb71c161a42e44a9fa8227abe61fa5c60ebe0 md5: cd5a90476766d53e901500df9215e927 @@ -757,16 +742,15 @@ depends: license: HPND size: 435273 timestamp: 1762022005702 -- conda: https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.41.3-h5347b49_0.conda -sha256: 1a7539cfa7df00714e8943e18de0b06cceef6778e420a5ee3a2a145773758aee -md5: db409b7c1720428638e7c0d509d3e1b5 +- conda: https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.42.1-h5347b49_0.conda +sha256: 3f0edf1280e2f6684a986f821eaa3e123d2694a00b31b96ca0d4a4c12c129231 +md5: 7d0a66598195ef00b6efc55aefc7453b depends: - __glibc >=2.17,<3.0.a0 - libgcc >=14 license: BSD-3-Clause -license_family: BSD -size: 40311 -timestamp: 1766271528534 +size: 40163 +timestamp: 1779118517630 - conda: https://conda.anaconda.org/conda-forge/linux-64/libwebp-base-1.6.0-hd42ef1d_0.conda sha256: 3aed21ab28eddffdaf7f804f49be7a7d701e8f0e46c856d801270b470820a37b md5: aea31d2e5b1091feca96fcfe945c3cf9 @@ -814,16 +798,16 @@ license: BSD-3-Clause license_family: BSD size: 85893 timestamp: 1770694658918 -- conda: https://conda.anaconda.org/conda-forge/noarch/markdown-it-py-4.0.0-pyhd8ed1ab_0.conda -sha256: 7b1da4b5c40385791dbc3cc85ceea9fad5da680a27d5d3cb8bfaa185e304a89e -md5: 5b5203189eb668f042ac2b0826244964 +- conda: https://conda.anaconda.org/conda-forge/noarch/markdown-it-py-4.2.0-pyhd8ed1ab_0.conda +sha256: 0c4c35376fe920714390d46e4b8d31c876d65f18e1655899e0763ec25f2a902f +md5: 6d03368f2b2b0a5fb6839df53b2eb5e0 depends: - mdurl >=0.1,<1 - python >=3.10 license: MIT license_family: MIT -size: 64736 -timestamp: 1754951288511 +size: 69017 +timestamp: 1778169663339 - conda: https://conda.anaconda.org/conda-forge/linux-64/markupsafe-3.0.3-py314h67df5f8_1.conda sha256: c279be85b59a62d5c52f5dd9a4cd43ebd08933809a8416c22c3131595607d4cf md5: 9a17c4307d23318476d7fbf0fedc0cde @@ -854,9 +838,9 @@ license: MIT license_family: MIT size: 14465 timestamp: 1733255681319 -- conda: https://conda.anaconda.org/bioconda/noarch/multiqc-1.33-pyhdfd78af_0.conda -sha256: f005760b13093362fc9c997d603dd487de32ab2e821a3cbce52a42bcb8136517 -md5: 698a8a27c2b9d8a542c70cb47099a75e +- conda: https://conda.anaconda.org/bioconda/noarch/multiqc-1.35-pyhdfd78af_0.conda +sha256: 5267ddcc9119b8bdfdddd83fa4713edf6e956443f7369ebd686dc6d9f921a428 +md5: d95457757ad503af93145630ec6e8965 depends: - click - coloredlogs @@ -870,10 +854,10 @@ depends: - packaging - pillow >=10.2.0 - plotly >=5.18 -- polars-lts-cpu +- polars >=1.34.0 - pyaml-env - pydantic >=2.7.1 -- python >=3.8,!=3.14.1 +- python >=3.9,!=3.14.1 - python-dotenv - python-kaleido 0.2.1 - pyyaml >=4 @@ -883,20 +867,21 @@ depends: - spectra >=0.0.10 - tiktoken - tqdm -- typeguard +- typeguard >=4 license: GPL-3.0-or-later license_family: GPL3 -size: 4198799 -timestamp: 1765300743879 -- conda: https://conda.anaconda.org/conda-forge/noarch/narwhals-2.18.1-pyhcf101f3_1.conda -sha256: 541fd4390a0687228b8578247f1536a821d9261389a65585af9d1a6f2a14e1e0 -md5: 30bec5e8f4c3969e2b1bd407c5e52afb +size: 4229065 +timestamp: 1778635617929 +- conda: https://conda.anaconda.org/conda-forge/noarch/narwhals-2.21.2-pyhcf101f3_0.conda +sha256: 70f43d62450927d51673eecd8823e14f5b3cfebdb43cda1d502eba97162bab42 +md5: 6687827c332121727ce383919e1ec8c2 depends: - python >=3.10 - python license: MIT -size: 280459 -timestamp: 1774380620329 +license_family: MIT +size: 284323 +timestamp: 1778929680962 - conda: https://conda.anaconda.org/conda-forge/noarch/natsort-8.4.0-pyhcf101f3_2.conda sha256: aeb1548eb72e4f198e72f19d242fb695b35add2ac7b2c00e0d83687052867680 md5: e941e85e273121222580723010bd4fa2 @@ -907,15 +892,15 @@ license: MIT license_family: MIT size: 39262 timestamp: 1770905275632 -- conda: https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h2d0b736_3.conda -sha256: 3fde293232fa3fca98635e1167de6b7c7fda83caf24b9d6c91ec9eefb4f4d586 -md5: 47e340acb35de30501a76c7c799c41d7 +- conda: https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.6-hdb14827_0.conda +sha256: fc89f74bbe362fb29fa3c037697a89bec140b346a2469a90f7936d1d7ea4d8a3 +md5: fc21868a1a5aacc937e7a18747acb8a5 depends: - __glibc >=2.17,<3.0.a0 -- libgcc >=13 +- libgcc >=14 license: X11 AND BSD-3-Clause -size: 891641 -timestamp: 1738195959188 +size: 918956 +timestamp: 1777422145199 - conda: https://conda.anaconda.org/conda-forge/noarch/networkx-3.6.1-pyhcf101f3_0.conda sha256: f6a82172afc50e54741f6f84527ef10424326611503c64e359e25a19a8e4c1c6 md5: a2c1eeadae7a309daed9d62c96012a2b @@ -956,24 +941,24 @@ license: MPL-2.0 license_family: MOZILLA size: 2057773 timestamp: 1763485556350 -- conda: https://conda.anaconda.org/conda-forge/linux-64/numpy-2.4.3-py314h2b28147_0.conda -sha256: f2ba8cb0d86a6461a6bcf0d315c80c7076083f72c6733c9290086640723f79ec -md5: 36f5b7eb328bdc204954a2225cf908e2 +- conda: https://conda.anaconda.org/conda-forge/linux-64/numpy-2.4.5-py314h2b28147_0.conda +sha256: 8e796bac2558ff5f2d00a2d0bbe4821d518347a8f70afb53b5acf27adb135197 +md5: 64a8d5cd0553d51590a304a28c184785 depends: - python - libstdcxx >=14 - libgcc >=14 - __glibc >=2.17,<3.0.a0 -- python_abi 3.14.* *_cp314 -- libcblas >=3.9.0,<4.0a0 - liblapack >=3.9.0,<4.0a0 +- python_abi 3.14.* *_cp314 - libblas >=3.9.0,<4.0a0 +- libcblas >=3.9.0,<4.0a0 constrains: - numpy-base <0a0 license: BSD-3-Clause license_family: BSD -size: 8927860 -timestamp: 1773839233468 +size: 8930431 +timestamp: 1778894356567 - conda: https://conda.anaconda.org/conda-forge/linux-64/openjpeg-2.5.4-h55fea9a_0.conda sha256: 3900f9f2dbbf4129cf3ad6acf4e4b6f7101390b53843591c53b00f034343bc4d md5: 11b3379b191f63139e29c0d19dee24cd @@ -988,48 +973,48 @@ license: BSD-2-Clause license_family: BSD size: 355400 timestamp: 1758489294972 -- conda: https://conda.anaconda.org/conda-forge/linux-64/openssl-3.6.1-h35e630c_1.conda -sha256: 44c877f8af015332a5d12f5ff0fb20ca32f896526a7d0cdb30c769df1144fb5c -md5: f61eb8cd60ff9057122a3d338b99c00f +- conda: https://conda.anaconda.org/conda-forge/linux-64/openssl-3.6.2-h35e630c_0.conda +sha256: c0ef482280e38c71a08ad6d71448194b719630345b0c9c60744a2010e8a8e0cb +md5: da1b85b6a87e141f5140bb9924cecab0 depends: - __glibc >=2.17,<3.0.a0 - ca-certificates - libgcc >=14 license: Apache-2.0 license_family: Apache -size: 3164551 -timestamp: 1769555830639 -- conda: https://conda.anaconda.org/conda-forge/noarch/packaging-26.0-pyhcf101f3_0.conda -sha256: c1fc0f953048f743385d31c468b4a678b3ad20caffdeaa94bed85ba63049fd58 -md5: b76541e68fea4d511b1ac46a28dcd2c6 +size: 3167099 +timestamp: 1775587756857 +- conda: https://conda.anaconda.org/conda-forge/noarch/packaging-26.2-pyhc364b38_0.conda +sha256: 3906abfb6511a3bb309e39b9b1b7bc38f50a723971de2395489fd1f379255890 +md5: 4c06a92e74452cfa53623a81592e8934 depends: - python >=3.8 - python license: Apache-2.0 license_family: APACHE -size: 72010 -timestamp: 1769093650580 -- conda: https://conda.anaconda.org/conda-forge/linux-64/pillow-12.1.1-py314h8ec4b1a_0.conda -sha256: 9e6ec8f3213e8b7d64b0ad45f84c51a2c9eba4398efda31e196c9a56186133ee -md5: 79678378ae235e24b3aa83cee1b38207 +size: 91574 +timestamp: 1777103621679 +- conda: https://conda.anaconda.org/conda-forge/linux-64/pillow-12.2.0-py314h8ec4b1a_0.conda +sha256: 123d8a7c16c88658b4f29e9f115a047598c941708dade74fbaff373a32dbec5e +md5: 76c4757c0ec9d11f969e8eb44899307b depends: - python - libgcc >=14 - __glibc >=2.17,<3.0.a0 +- libtiff >=4.7.1,<4.8.0a0 +- openjpeg >=2.5.4,<3.0a0 +- libxcb >=1.17.0,<2.0a0 - libwebp-base >=1.6.0,<2.0a0 - zlib-ng >=2.3.3,<2.4.0a0 -- python_abi 3.14.* *_cp314 -- tk >=8.6.13,<8.7.0a0 - libjpeg-turbo >=3.1.2,<4.0a0 -- libxcb >=1.17.0,<2.0a0 -- openjpeg >=2.5.4,<3.0a0 +- python_abi 3.14.* *_cp314 +- libfreetype >=2.14.3 +- libfreetype6 >=2.14.3 - lcms2 >=2.18,<3.0a0 -- libtiff >=4.7.1,<4.8.0a0 -- libfreetype >=2.14.1 -- libfreetype6 >=2.14.1 +- tk >=8.6.13,<8.7.0a0 license: HPND -size: 1073026 -timestamp: 1770794002408 +size: 1082797 +timestamp: 1775060059882 - conda: https://conda.anaconda.org/conda-forge/noarch/plotly-6.6.0-pyhd8ed1ab_0.conda sha256: c418d325359fc7a0074cea7f081ef1bce26e114d2da8a0154c5d27ecc87a08e7 md5: 3e9427ee186846052e81fadde8ebe96a @@ -1043,11 +1028,11 @@ license: MIT license_family: MIT size: 5251872 timestamp: 1772628857717 -- conda: https://conda.anaconda.org/conda-forge/noarch/polars-1.39.3-pyh58ad624_1.conda -sha256: d332c2d5002fc440ae37ed9679ffc21b552f18d20232390005d1dd3bce0888d3 -md5: d5a4e013a30dd8dfde9ab39f45aaf9c1 +- conda: https://conda.anaconda.org/conda-forge/noarch/polars-1.40.1-pyh58ad624_1.conda +sha256: 83e37ede46e8e57d4785e804604a88fa02d6eac9a774cee40d49018f9da9ead1 +md5: bdbac766376390889b74216b70206af4 depends: -- polars-runtime-32 ==1.39.3 +- polars-runtime-32 ==1.40.1 - python >=3.10 - python constrains: @@ -1061,44 +1046,17 @@ constrains: - pyiceberg >=0.7.1 - altair >=5.4.0 - great_tables >=0.8.0 -- polars-runtime-32 ==1.39.3 -- polars-runtime-64 ==1.39.3 -- polars-runtime-compat ==1.39.3 -license: MIT -license_family: MIT -size: 533495 -timestamp: 1774207987966 -- conda: https://conda.anaconda.org/conda-forge/noarch/polars-lts-cpu-1.34.0.deprecated-hc364b38_0.conda -sha256: e466fb31f67ba9bde18deafeb34263ca5eb25807f39ead0e9d753a8e82c4c4f4 -md5: ef0340e75068ac8ff96462749b5c98e7 -depends: -- polars >=1.34.0 -- polars-runtime-compat >=1.34.0 -license: MIT -license_family: MIT -size: 3902 -timestamp: 1760206808444 -- conda: https://conda.anaconda.org/conda-forge/linux-64/polars-runtime-32-1.39.3-py310hffdcd12_1.conda -noarch: python -sha256: 9744f8086bb0832998f5b01076f57ddc9efbe460e493b14303c3567dc4f401e7 -md5: f9327f9f2cfc4215f55b613e64afd3ba -depends: -- python -- libstdcxx >=14 -- libgcc >=14 -- __glibc >=2.17,<3.0.a0 -- _python_abi3_support 1.* -- cpython >=3.10 -constrains: -- __glibc >=2.17 +- polars-runtime-32 ==1.40.1 +- polars-runtime-64 ==1.40.1 +- polars-runtime-compat ==1.40.1 license: MIT license_family: MIT -size: 37570276 -timestamp: 1774207987966 -- conda: https://conda.anaconda.org/conda-forge/linux-64/polars-runtime-compat-1.39.3-py310hbcd5346_1.conda +size: 539000 +timestamp: 1778779696741 +- conda: https://conda.anaconda.org/conda-forge/linux-64/polars-runtime-32-1.40.1-py310h49dadd8_1.conda noarch: python -sha256: bf0b932713f0f27924f42159c98426e0073bb6145ed796eaa4cec79ca05363c7 -md5: 4b9b312453eebd6fbdbbe2a88fa1b5c4 +sha256: c163631030b3c53174019e577ffaa9c83dab3bbaa1e6336001c5ed2faae364ba +md5: 5072dd8db4336777a95a1dd12e24623a depends: - python - libgcc >=14 @@ -1110,8 +1068,8 @@ constrains: - __glibc >=2.17 license: MIT license_family: MIT -size: 37224264 -timestamp: 1774207985377 +size: 42001857 +timestamp: 1778779696741 - conda: https://conda.anaconda.org/conda-forge/linux-64/procps-ng-4.0.6-h18c060e_0.conda sha256: 4ce2e1ee31a6217998f78c31ce7dc0a3e0557d9238b51d49dd20c52d467a126d md5: f2c23a77b25efcad57d377b34bd84941 @@ -1143,24 +1101,23 @@ license: MIT license_family: MIT size: 14645 timestamp: 1736766960536 -- conda: https://conda.anaconda.org/conda-forge/noarch/pydantic-2.12.5-pyhcf101f3_1.conda -sha256: 868569d9505b7fe246c880c11e2c44924d7613a8cdcc1f6ef85d5375e892f13d -md5: c3946ed24acdb28db1b5d63321dbca7d +- conda: https://conda.anaconda.org/conda-forge/noarch/pydantic-2.13.4-pyhcf101f3_0.conda +sha256: 69700e31165df070e9716315e042196aa92525dae5deb5107785847ab9f4189f +md5: 729843edafc0899b3348bd3f19525b9d depends: - typing-inspection >=0.4.2 - typing_extensions >=4.14.1 - python >=3.10 -- typing-extensions >=4.6.1 - annotated-types >=0.6.0 -- pydantic-core ==2.41.5 +- pydantic-core ==2.46.4 - python license: MIT license_family: MIT -size: 340482 -timestamp: 1764434463101 -- conda: https://conda.anaconda.org/conda-forge/linux-64/pydantic-core-2.41.5-py314h2e6c369_1.conda -sha256: 7e0ae379796e28a429f8e48f2fe22a0f232979d65ec455e91f8dac689247d39f -md5: 432b0716a1dfac69b86aa38fdd59b7e6 +size: 346511 +timestamp: 1778103405862 +- conda: https://conda.anaconda.org/conda-forge/linux-64/pydantic-core-2.46.4-py314h2e6c369_0.conda +sha256: 802e216c39f1359aed60823b6e11d8ccd812b0ae1c81ae5ac1c81f99446409ab +md5: 0c96993dbeadf3a277cf757b9f1c9412 depends: - python - typing-extensions >=4.6.0,!=4.7.0 @@ -1171,17 +1128,17 @@ constrains: - __glibc >=2.17 license: MIT license_family: MIT -size: 1943088 -timestamp: 1762988995556 -- conda: https://conda.anaconda.org/conda-forge/noarch/pygments-2.19.2-pyhd8ed1ab_0.conda -sha256: 5577623b9f6685ece2697c6eb7511b4c9ac5fb607c9babc2646c811b428fd46a -md5: 6b6ece66ebcae2d5f326c77ef2c5a066 +size: 1895020 +timestamp: 1778084229247 +- conda: https://conda.anaconda.org/conda-forge/noarch/pygments-2.20.0-pyhd8ed1ab_0.conda +sha256: cf70b2f5ad9ae472b71235e5c8a736c9316df3705746de419b59d442e8348e86 +md5: 16c18772b340887160c79a6acc022db0 depends: -- python >=3.9 +- python >=3.10 license: BSD-2-Clause license_family: BSD -size: 889287 -timestamp: 1750615908735 +size: 893031 +timestamp: 1774796815820 - conda: https://conda.anaconda.org/conda-forge/noarch/pysocks-1.7.1-pyha55dd90_7.conda sha256: ba3b032fa52709ce0d9fd388f63d330a026754587a2f461117cac9ab73d8d0d8 md5: 461219d1a5bd61342293efa2c0c90eac @@ -1192,32 +1149,32 @@ license: BSD-3-Clause license_family: BSD size: 21085 timestamp: 1733217331982 -- conda: https://conda.anaconda.org/conda-forge/linux-64/python-3.14.3-h32b2ec7_101_cp314.conda -build_number: 101 -sha256: cb0628c5f1732f889f53a877484da98f5a0e0f47326622671396fb4f2b0cd6bd -md5: c014ad06e60441661737121d3eae8a60 +- conda: https://conda.anaconda.org/conda-forge/linux-64/python-3.14.4-habeac84_100_cp314.conda +build_number: 100 +sha256: dec247c5badc811baa34d6085df9d0465535883cf745e22e8d79092ad54a3a7b +md5: a443f87920815d41bfe611296e507995 depends: - __glibc >=2.17,<3.0.a0 - bzip2 >=1.0.8,<2.0a0 - ld_impl_linux-64 >=2.36.1 -- libexpat >=2.7.3,<3.0a0 +- libexpat >=2.7.5,<3.0a0 - libffi >=3.5.2,<3.6.0a0 - libgcc >=14 - liblzma >=5.8.2,<6.0a0 - libmpdec >=4.0.0,<5.0a0 -- libsqlite >=3.51.2,<4.0a0 -- libuuid >=2.41.3,<3.0a0 -- libzlib >=1.3.1,<2.0a0 +- libsqlite >=3.52.0,<4.0a0 +- libuuid >=2.42,<3.0a0 +- libzlib >=1.3.2,<2.0a0 - ncurses >=6.5,<7.0a0 -- openssl >=3.5.5,<4.0a0 +- openssl >=3.5.6,<4.0a0 - python_abi 3.14.* *_cp314 - readline >=8.3,<9.0a0 - tk >=8.6.13,<8.7.0a0 - tzdata - zstd >=1.5.7,<1.6.0a0 license: Python-2.0 -size: 36702440 -timestamp: 1770675584356 +size: 36705460 +timestamp: 1775614357822 python_site_packages_path: lib/python3.14/site-packages - conda: https://conda.anaconda.org/conda-forge/noarch/python-dotenv-1.2.2-pyhcf101f3_0.conda sha256: 74e417a768f59f02a242c25e7db0aa796627b5bc8c818863b57786072aeb85e5 @@ -1228,15 +1185,15 @@ license: BSD-3-Clause license_family: BSD size: 27848 timestamp: 1772388605021 -- conda: https://conda.anaconda.org/conda-forge/noarch/python-gil-3.14.3-h4df99d1_101.conda -sha256: 233aebd94c704ac112afefbb29cf4170b7bc606e22958906f2672081bc50638a -md5: 235765e4ea0d0301c75965985163b5a1 +- conda: https://conda.anaconda.org/conda-forge/noarch/python-gil-3.14.4-h4df99d1_100.conda +sha256: 36ff7984e4565c85149e64f8206303d412a0652e55cf806dcb856903fa056314 +md5: e4e60721757979d01d3964122f674959 depends: -- cpython 3.14.3.* +- cpython 3.14.4.* - python_abi * *_cp314 license: Python-2.0 -size: 50062 -timestamp: 1770674497152 +size: 49806 +timestamp: 1775614307464 - conda: https://conda.anaconda.org/conda-forge/noarch/python-kaleido-0.2.1-pyhd8ed1ab_0.tar.bz2 sha256: e17bf63a30aec33432f1ead86e15e9febde9fc40a7f869c0e766be8d2db44170 md5: 310259a5b03ff02289d7705f39e2b1d2 @@ -1294,9 +1251,9 @@ license: MIT license_family: MIT size: 51788 timestamp: 1760379115194 -- conda: https://conda.anaconda.org/conda-forge/linux-64/regex-2026.2.28-py314h5bd0f2a_0.conda -sha256: e085e336f1446f5263a3ec9747df8c719b6996753901181add50dc4fdd8bb2e8 -md5: 3c8b6a8c4d0ff5a264e9831eac4941f4 +- conda: https://conda.anaconda.org/conda-forge/linux-64/regex-2026.5.9-py314h5bd0f2a_0.conda +sha256: c7a4aca4977c15c82d053b06cbc676460974c1b25757cfeea8a9a2497ac911f8 +md5: 9dd235b6ac69a0198080dac39f9891aa depends: - __glibc >=2.17,<3.0.a0 - libgcc >=14 @@ -1304,27 +1261,27 @@ depends: - python_abi 3.14.* *_cp314 license: Apache-2.0 AND CNRI-Python license_family: PSF -size: 411924 -timestamp: 1772255161535 -- conda: https://conda.anaconda.org/conda-forge/noarch/requests-2.32.5-pyhcf101f3_1.conda -sha256: 7813c38b79ae549504b2c57b3f33394cea4f2ad083f0994d2045c2e24cb538c5 -md5: c65df89a0b2e321045a9e01d1337b182 +size: 413611 +timestamp: 1778374155646 +- conda: https://conda.anaconda.org/conda-forge/noarch/requests-2.34.2-pyhcf101f3_0.conda +sha256: 1715246b19c9f85ee022933b4845f2fc14ac9184981b7b7d9b728bec8e9588da +md5: 4a85203c1d80c1059086ae860836ffb9 depends: - python >=3.10 -- certifi >=2017.4.17 +- certifi >=2023.5.7 - charset-normalizer >=2,<4 - idna >=2.5,<4 -- urllib3 >=1.21.1,<3 +- urllib3 >=1.26,<3 - python constrains: -- chardet >=3.0.2,<6 +- chardet >=3.0.2,<8 license: Apache-2.0 license_family: APACHE -size: 63602 -timestamp: 1766926974520 -- conda: https://conda.anaconda.org/conda-forge/noarch/rich-14.3.3-pyhcf101f3_0.conda -sha256: b06ce84d6a10c266811a7d3adbfa1c11f13393b91cc6f8a5b468277d90be9590 -md5: 7a6289c50631d620652f5045a63eb573 +size: 68709 +timestamp: 1778851103479 +- conda: https://conda.anaconda.org/conda-forge/noarch/rich-15.0.0-pyhcf101f3_0.conda +sha256: 3d6ba2c0fcdac3196ba2f0615b4104e532525ffa1335b50a2878be5ff488814a +md5: 0242025a3c804966bf71aa04eee82f66 depends: - markdown-it-py >=2.2.0 - pygments >=2.13.0,<3.0.0 @@ -1333,8 +1290,8 @@ depends: - python license: MIT license_family: MIT -size: 208472 -timestamp: 1771572730357 +size: 208577 +timestamp: 1775991661559 - conda: https://conda.anaconda.org/conda-forge/noarch/rich-click-1.9.7-pyh8f84b5b_0.conda sha256: aa3fcb167321bae51998de2e94d199109c9024f25a5a063cb1c28d8f1af33436 md5: 0c20a8ebcddb24a45da89d5e917e6cb9 @@ -1373,20 +1330,19 @@ license: MIT license_family: MIT size: 22284 timestamp: 1735770589188 -- conda: https://conda.anaconda.org/conda-forge/linux-64/sqlite-3.52.0-h04a0ce9_0.conda -sha256: c9af81e7830d9c4b67a7f48e512d060df2676b29cac59e3b31f09dbfcee29c58 -md5: 7d9d7efe9541d4bb71b5934e8ee348ea +- conda: https://conda.anaconda.org/conda-forge/linux-64/sqlite-3.53.1-hbc0de68_0.conda +sha256: d167fa92781bcdcd3b9aaa6bb1cd50c5b108f6190c170098a118b5cf5df2f881 +md5: 8e0b8654ead18e50af552e54b5a08a61 depends: - __glibc >=2.17,<3.0.a0 -- icu >=78.2,<79.0a0 - libgcc >=14 -- libsqlite 3.52.0 hf4e2dac_0 -- libzlib >=1.3.1,<2.0a0 -- ncurses >=6.5,<7.0a0 +- libsqlite 3.53.1 h0c1763c_0 +- libzlib >=1.3.2,<2.0a0 +- ncurses >=6.6,<7.0a0 - readline >=8.3,<9.0a0 license: blessing -size: 203641 -timestamp: 1772818888368 +size: 205399 +timestamp: 1777986477546 - conda: https://conda.anaconda.org/conda-forge/linux-64/tiktoken-0.12.0-py314h67fec18_3.conda sha256: 7e395d67fd249d901beb1ae269057763c0d8c3ee5f7a348694bdb16d158a37d9 md5: d705f9d8a1185a2b01cced191177a028 @@ -1427,20 +1383,20 @@ depends: license: MPL-2.0 and MIT size: 94132 timestamp: 1770153424136 -- conda: https://conda.anaconda.org/conda-forge/noarch/typeguard-4.5.1-pyhd8ed1ab_0.conda -sha256: 39d8ae33c43cdb8f771373e149b0b4fae5a08960ac58dcca95b2f1642bb17448 -md5: 260af1b0a94f719de76b4e14094e9a3b +- conda: https://conda.anaconda.org/conda-forge/noarch/typeguard-4.5.2-pyhcf101f3_0.conda +sha256: 59d7851d32fddb5b510272e6557aa982edeb927d349648dac27f5bf01d18bb26 +md5: 4460f039b7dedf15f7df086446ca75ae depends: -- importlib-metadata >=3.6 -- python >=3.10 -- typing-extensions >=4.10.0 - typing_extensions >=4.14.0 +- python >=3.10 +- importlib-metadata >=3.6 +- python constrains: - pytest >=7 license: MIT license_family: MIT -size: 36838 -timestamp: 1771532971545 +size: 38297 +timestamp: 1778779291237 - conda: https://conda.anaconda.org/conda-forge/noarch/typing-extensions-4.15.0-h396c80c_0.conda sha256: 7c2df5721c742c2a47b2c8f960e718c930031663ac1174da67c1ed5999f7938c md5: edd329d7d3a4ab45dcf905899a7a6115 @@ -1450,16 +1406,17 @@ license: PSF-2.0 license_family: PSF size: 91383 timestamp: 1756220668932 -- conda: https://conda.anaconda.org/conda-forge/noarch/typing-inspection-0.4.2-pyhd8ed1ab_1.conda -sha256: 70db27de58a97aeb7ba7448366c9853f91b21137492e0b4430251a1870aa8ff4 -md5: a0a4a3035667fc34f29bfbd5c190baa6 +- conda: https://conda.anaconda.org/conda-forge/noarch/typing-inspection-0.4.2-pyhcf101f3_2.conda +sha256: 8b90d2f19f9458b8c58a55e1fcdc1d90c1603a847a47654d8a454549413ba60a +md5: 53f5409c5cfd6c5a66417d68e3f0a864 depends: - python >=3.10 - typing_extensions >=4.12.0 +- python license: MIT license_family: MIT -size: 18923 -timestamp: 1764158430324 +size: 20935 +timestamp: 1777105465795 - conda: https://conda.anaconda.org/conda-forge/noarch/typing_extensions-4.15.0-pyhcf101f3_0.conda sha256: 032271135bca55aeb156cee361c81350c6f3fb203f57d024d7e5a1fc9ef18731 md5: 0caa1af407ecff61170c9437a808404d @@ -1476,9 +1433,9 @@ md5: ad659d0a2b3e47e38d829aa8cad2d610 license: LicenseRef-Public-Domain size: 119135 timestamp: 1767016325805 -- conda: https://conda.anaconda.org/conda-forge/noarch/urllib3-2.6.3-pyhd8ed1ab_0.conda -sha256: af641ca7ab0c64525a96fd9ad3081b0f5bcf5d1cbb091afb3f6ed5a9eee6111a -md5: 9272daa869e03efe68833e3dc7a02130 +- conda: https://conda.anaconda.org/conda-forge/noarch/urllib3-2.7.0-pyhd8ed1ab_0.conda +sha256: feff959a816f7988a0893201aa9727bbb7ee1e9cec2c4f0428269b489eb93fb4 +md5: cbb88288f74dbe6ada1c6c7d0a97223e depends: - backports.zstd >=1.0.0 - brotli-python >=1.2.0 @@ -1487,8 +1444,8 @@ depends: - python >=3.10 license: MIT license_family: MIT -size: 103172 -timestamp: 1767817860341 +size: 103560 +timestamp: 1778188657149 - conda: https://conda.anaconda.org/conda-forge/linux-64/xorg-libxau-1.0.12-hb03c661_1.conda sha256: 6bc6ab7a90a5d8ac94c7e300cc10beb0500eeba4b99822768ca2f2ef356f731b md5: b2895afaf55bf96a8c8282a2e47a5de0 @@ -1519,16 +1476,16 @@ license: MIT license_family: MIT size: 85189 timestamp: 1753484064210 -- conda: https://conda.anaconda.org/conda-forge/noarch/zipp-3.23.0-pyhcf101f3_1.conda -sha256: b4533f7d9efc976511a73ef7d4a2473406d7f4c750884be8e8620b0ce70f4dae -md5: 30cd29cb87d819caead4d55184c1d115 +- conda: https://conda.anaconda.org/conda-forge/noarch/zipp-4.1.0-pyhcf101f3_0.conda +sha256: 210bd31c22bb88f5e2a167df24c95bb5f152b2ada7502f9b8c49d1f5366db423 +md5: ba3dcdc8584155c97c648ae9c044b7a3 depends: - python >=3.10 - python license: MIT license_family: MIT -size: 24194 -timestamp: 1764460141901 +size: 24190 +timestamp: 1779159948016 - conda: https://conda.anaconda.org/conda-forge/linux-64/zlib-ng-2.3.3-hceb46e0_1.conda sha256: ea4e50c465d70236408cb0bfe0115609fd14db1adcd8bd30d8918e0291f8a75f md5: 2aadb0d17215603a82a2a6b0afd9a4cb diff --git a/modules/nf-core/multiqc/.conda-lock/linux_arm64-bd-40bf3b435e89dc22_1.txt b/modules/nf-core/multiqc/.conda-lock/linux_arm64-bd-3e45d17b40a576b4_1.txt similarity index 75% rename from modules/nf-core/multiqc/.conda-lock/linux_arm64-bd-40bf3b435e89dc22_1.txt rename to modules/nf-core/multiqc/.conda-lock/linux_arm64-bd-3e45d17b40a576b4_1.txt index a58231a0..492ce480 100644 --- a/modules/nf-core/multiqc/.conda-lock/linux_arm64-bd-40bf3b435e89dc22_1.txt +++ b/modules/nf-core/multiqc/.conda-lock/linux_arm64-bd-3e45d17b40a576b4_1.txt @@ -14,17 +14,17 @@ linux-aarch64: - conda: https://conda.anaconda.org/conda-forge/noarch/_python_abi3_support-1.0-hd8ed1ab_2.conda - conda: https://conda.anaconda.org/conda-forge/noarch/annotated-types-0.7.0-pyhd8ed1ab_1.conda - conda: https://conda.anaconda.org/conda-forge/noarch/attrs-26.1.0-pyhcf101f3_0.conda -- conda: https://conda.anaconda.org/conda-forge/noarch/backports.zstd-1.3.0-py314h680f03e_0.conda +- conda: https://conda.anaconda.org/conda-forge/noarch/backports.zstd-1.5.0-py314h680f03e_0.conda - conda: https://conda.anaconda.org/conda-forge/linux-aarch64/brotli-python-1.2.0-py314h352cb57_1.conda - conda: https://conda.anaconda.org/conda-forge/linux-aarch64/bzip2-1.0.8-h4777abc_9.conda -- conda: https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2026.2.25-hbd8a1cb_0.conda -- conda: https://conda.anaconda.org/conda-forge/noarch/certifi-2026.2.25-pyhd8ed1ab_0.conda -- conda: https://conda.anaconda.org/conda-forge/noarch/charset-normalizer-3.4.6-pyhd8ed1ab_0.conda -- conda: https://conda.anaconda.org/conda-forge/noarch/click-8.3.1-pyh8f84b5b_1.conda +- conda: https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2026.4.22-hbd8a1cb_0.conda +- conda: https://conda.anaconda.org/conda-forge/noarch/certifi-2026.4.22-pyhd8ed1ab_0.conda +- conda: https://conda.anaconda.org/conda-forge/noarch/charset-normalizer-3.4.7-pyhd8ed1ab_0.conda +- conda: https://conda.anaconda.org/conda-forge/noarch/click-8.4.0-pyhc90fa1f_0.conda - conda: https://conda.anaconda.org/conda-forge/noarch/coloredlogs-15.0.1-pyhd8ed1ab_4.conda - conda: https://conda.anaconda.org/conda-forge/noarch/colormath-3.0.0-pyhd8ed1ab_4.conda -- conda: https://conda.anaconda.org/conda-forge/noarch/cpython-3.14.3-py314hd8ed1ab_101.conda -- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/expat-2.7.4-hfae3067_0.conda +- conda: https://conda.anaconda.org/conda-forge/noarch/cpython-3.14.4-py314hd8ed1ab_100.conda +- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/expat-2.8.0-hfae3067_0.conda - conda: https://conda.anaconda.org/conda-forge/noarch/font-ttf-dejavu-sans-mono-2.37-hab24e00_0.tar.bz2 - conda: https://conda.anaconda.org/conda-forge/noarch/font-ttf-inconsolata-3.000-h77eed37_0.tar.bz2 - conda: https://conda.anaconda.org/conda-forge/noarch/font-ttf-source-code-pro-2.038-h77eed37_0.tar.bz2 @@ -36,98 +36,95 @@ linux-aarch64: - conda: https://conda.anaconda.org/conda-forge/noarch/humanfriendly-10.0-pyh707e725_8.conda - conda: https://conda.anaconda.org/conda-forge/noarch/humanize-4.15.0-pyhd8ed1ab_0.conda - conda: https://conda.anaconda.org/conda-forge/noarch/hyperframe-6.1.0-pyhd8ed1ab_0.conda -- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/icu-78.3-hcab7f73_0.conda -- conda: https://conda.anaconda.org/conda-forge/noarch/idna-3.11-pyhd8ed1ab_0.conda +- conda: https://conda.anaconda.org/conda-forge/noarch/idna-3.13-pyhcf101f3_0.conda - conda: https://conda.anaconda.org/conda-forge/noarch/importlib-metadata-8.8.0-pyhcf101f3_0.conda - conda: https://conda.anaconda.org/conda-forge/noarch/jinja2-3.1.6-pyhcf101f3_1.conda - conda: https://conda.anaconda.org/conda-forge/noarch/jsonschema-4.26.0-pyhcf101f3_0.conda - conda: https://conda.anaconda.org/conda-forge/noarch/jsonschema-specifications-2025.9.1-pyhcf101f3_0.conda - conda: https://conda.anaconda.org/conda-forge/linux-aarch64/kaleido-core-0.2.1-he5a581e_0.tar.bz2 -- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/lcms2-2.18-h9d5b58d_0.conda +- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/lcms2-2.19.1-h9d5b58d_0.conda - conda: https://conda.anaconda.org/conda-forge/linux-aarch64/ld_impl_linux-aarch64-2.45.1-default_h1979696_102.conda - conda: https://conda.anaconda.org/conda-forge/linux-aarch64/lerc-4.1.0-h52b7260_0.conda -- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/libblas-3.11.0-5_haddc8a3_openblas.conda -- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/libcblas-3.11.0-5_hd72aa62_openblas.conda +- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/libblas-3.11.0-7_haddc8a3_openblas.conda +- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/libcblas-3.11.0-7_hd72aa62_openblas.conda - conda: https://conda.anaconda.org/conda-forge/linux-aarch64/libdeflate-1.25-h1af38f5_0.conda -- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/libexpat-2.7.4-hfae3067_0.conda +- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/libexpat-2.8.0-hfae3067_0.conda - conda: https://conda.anaconda.org/conda-forge/linux-aarch64/libffi-3.5.2-h376a255_0.conda - conda: https://conda.anaconda.org/conda-forge/linux-aarch64/libfreetype-2.14.3-h8af1aa0_0.conda - conda: https://conda.anaconda.org/conda-forge/linux-aarch64/libfreetype6-2.14.3-hdae7a39_0.conda -- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/libgcc-15.2.0-h8acb6b2_18.conda -- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/libgcc-ng-15.2.0-he9431aa_18.conda -- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/libgfortran-15.2.0-he9431aa_18.conda -- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/libgfortran5-15.2.0-h1b7bec0_18.conda -- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/libgomp-15.2.0-h8acb6b2_18.conda -- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/libjpeg-turbo-3.1.2-he30d5cf_0.conda -- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/liblapack-3.11.0-5_h88aeb00_openblas.conda -- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/liblzma-5.8.2-he30d5cf_0.conda +- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/libgcc-15.2.0-h8acb6b2_19.conda +- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/libgcc-ng-15.2.0-he9431aa_19.conda +- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/libgfortran-15.2.0-he9431aa_19.conda +- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/libgfortran5-15.2.0-h1b7bec0_19.conda +- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/libgomp-15.2.0-h8acb6b2_19.conda +- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/libjpeg-turbo-3.1.4.1-he30d5cf_0.conda +- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/liblapack-3.11.0-7_h88aeb00_openblas.conda +- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/liblzma-5.8.3-he30d5cf_0.conda - conda: https://conda.anaconda.org/conda-forge/linux-aarch64/libmpdec-4.0.0-he30d5cf_1.conda -- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/libopenblas-0.3.30-pthreads_h9d3fd7e_4.conda -- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/libpng-1.6.55-h1abf092_0.conda -- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/libsqlite-3.52.0-h10b116e_0.conda -- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/libstdcxx-15.2.0-hef695bb_18.conda +- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/libopenblas-0.3.33-pthreads_h9d3fd7e_0.conda +- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/libpng-1.6.58-h1abf092_0.conda +- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/libsqlite-3.53.1-h022381a_0.conda +- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/libstdcxx-15.2.0-hef695bb_19.conda - conda: https://conda.anaconda.org/conda-forge/linux-aarch64/libtiff-4.7.1-hdb009f0_1.conda -- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/libuuid-2.41.3-h1022ec0_0.conda +- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/libuuid-2.42.1-h1022ec0_0.conda - conda: https://conda.anaconda.org/conda-forge/linux-aarch64/libwebp-base-1.6.0-ha2e29f5_0.conda - conda: https://conda.anaconda.org/conda-forge/linux-aarch64/libxcb-1.17.0-h262b8f6_0.conda - conda: https://conda.anaconda.org/conda-forge/linux-aarch64/libzlib-1.3.2-hdc9db2a_2.conda - conda: https://conda.anaconda.org/conda-forge/noarch/markdown-3.10.2-pyhcf101f3_0.conda -- conda: https://conda.anaconda.org/conda-forge/noarch/markdown-it-py-4.0.0-pyhd8ed1ab_0.conda +- conda: https://conda.anaconda.org/conda-forge/noarch/markdown-it-py-4.2.0-pyhd8ed1ab_0.conda - conda: https://conda.anaconda.org/conda-forge/linux-aarch64/markupsafe-3.0.3-py314hb76de3f_1.conda - conda: https://conda.anaconda.org/conda-forge/linux-aarch64/mathjax-2.7.7-h8af1aa0_3.tar.bz2 - conda: https://conda.anaconda.org/conda-forge/noarch/mdurl-0.1.2-pyhd8ed1ab_1.conda -- conda: https://conda.anaconda.org/bioconda/noarch/multiqc-1.33-pyhdfd78af_0.conda -- conda: https://conda.anaconda.org/conda-forge/noarch/narwhals-2.18.1-pyhcf101f3_1.conda +- conda: https://conda.anaconda.org/bioconda/noarch/multiqc-1.35-pyhdfd78af_0.conda +- conda: https://conda.anaconda.org/conda-forge/noarch/narwhals-2.21.2-pyhcf101f3_0.conda - conda: https://conda.anaconda.org/conda-forge/noarch/natsort-8.4.0-pyhcf101f3_2.conda -- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/ncurses-6.5-ha32ae93_3.conda +- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/ncurses-6.6-hf8d1292_0.conda - conda: https://conda.anaconda.org/conda-forge/noarch/networkx-3.6.1-pyhcf101f3_0.conda - conda: https://conda.anaconda.org/conda-forge/linux-aarch64/nspr-4.38-h3ad9384_0.conda - conda: https://conda.anaconda.org/conda-forge/linux-aarch64/nss-3.118-h544fa81_0.conda -- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/numpy-2.4.3-py314haac167e_0.conda +- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/numpy-2.4.5-py314he1698a1_0.conda - conda: https://conda.anaconda.org/conda-forge/linux-aarch64/openjpeg-2.5.4-h5da879a_0.conda -- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/openssl-3.6.1-h546c87b_1.conda -- conda: https://conda.anaconda.org/conda-forge/noarch/packaging-26.0-pyhcf101f3_0.conda -- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/pillow-12.1.1-py314hac3e5ec_0.conda +- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/openssl-3.6.2-h546c87b_0.conda +- conda: https://conda.anaconda.org/conda-forge/noarch/packaging-26.2-pyhc364b38_0.conda +- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/pillow-12.2.0-py314hac3e5ec_0.conda - conda: https://conda.anaconda.org/conda-forge/noarch/plotly-6.6.0-pyhd8ed1ab_0.conda -- conda: https://conda.anaconda.org/conda-forge/noarch/polars-1.39.3-pyh58ad624_1.conda -- conda: https://conda.anaconda.org/conda-forge/noarch/polars-lts-cpu-1.34.0.deprecated-hc364b38_0.conda -- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/polars-runtime-32-1.39.3-py310hff09b76_1.conda -- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/polars-runtime-compat-1.39.3-py310hf00a4a2_1.conda +- conda: https://conda.anaconda.org/conda-forge/noarch/polars-1.40.1-pyh58ad624_1.conda +- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/polars-runtime-32-1.40.1-py310h32c7c23_1.conda - conda: https://conda.anaconda.org/conda-forge/linux-aarch64/procps-ng-4.0.6-h1779866_0.conda - conda: https://conda.anaconda.org/conda-forge/linux-aarch64/pthread-stubs-0.4-h86ecc28_1002.conda - conda: https://conda.anaconda.org/conda-forge/noarch/pyaml-env-1.2.2-pyhd8ed1ab_0.conda -- conda: https://conda.anaconda.org/conda-forge/noarch/pydantic-2.12.5-pyhcf101f3_1.conda -- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/pydantic-core-2.41.5-py314h451b6cc_1.conda -- conda: https://conda.anaconda.org/conda-forge/noarch/pygments-2.19.2-pyhd8ed1ab_0.conda +- conda: https://conda.anaconda.org/conda-forge/noarch/pydantic-2.13.4-pyhcf101f3_0.conda +- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/pydantic-core-2.46.4-py314h451b6cc_0.conda +- conda: https://conda.anaconda.org/conda-forge/noarch/pygments-2.20.0-pyhd8ed1ab_0.conda - conda: https://conda.anaconda.org/conda-forge/noarch/pysocks-1.7.1-pyha55dd90_7.conda -- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/python-3.14.3-hb06a95a_101_cp314.conda +- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/python-3.14.4-hfd9ac0a_100_cp314.conda - conda: https://conda.anaconda.org/conda-forge/noarch/python-dotenv-1.2.2-pyhcf101f3_0.conda -- conda: https://conda.anaconda.org/conda-forge/noarch/python-gil-3.14.3-h4df99d1_101.conda +- conda: https://conda.anaconda.org/conda-forge/noarch/python-gil-3.14.4-h4df99d1_100.conda - conda: https://conda.anaconda.org/conda-forge/noarch/python-kaleido-0.2.1-pyhd8ed1ab_0.tar.bz2 - conda: https://conda.anaconda.org/conda-forge/noarch/python_abi-3.14-8_cp314.conda - conda: https://conda.anaconda.org/conda-forge/linux-aarch64/pyyaml-6.0.3-py314h807365f_1.conda - conda: https://conda.anaconda.org/conda-forge/linux-aarch64/readline-8.3-hb682ff5_0.conda - conda: https://conda.anaconda.org/conda-forge/noarch/referencing-0.37.0-pyhcf101f3_0.conda -- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/regex-2026.2.28-py314h51f160d_0.conda -- conda: https://conda.anaconda.org/conda-forge/noarch/requests-2.32.5-pyhcf101f3_1.conda -- conda: https://conda.anaconda.org/conda-forge/noarch/rich-14.3.3-pyhcf101f3_0.conda +- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/regex-2026.5.9-py314h51f160d_0.conda +- conda: https://conda.anaconda.org/conda-forge/noarch/requests-2.34.2-pyhcf101f3_0.conda +- conda: https://conda.anaconda.org/conda-forge/noarch/rich-15.0.0-pyhcf101f3_0.conda - conda: https://conda.anaconda.org/conda-forge/noarch/rich-click-1.9.7-pyh8f84b5b_0.conda - conda: https://conda.anaconda.org/conda-forge/linux-aarch64/rpds-py-0.30.0-py314h02b7a91_0.conda - conda: https://conda.anaconda.org/conda-forge/noarch/spectra-0.0.11-pyhd8ed1ab_2.conda -- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/sqlite-3.52.0-hf1c7be2_0.conda +- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/sqlite-3.53.1-he8854b5_0.conda - conda: https://conda.anaconda.org/conda-forge/linux-aarch64/tiktoken-0.12.0-py314h6a36e60_3.conda - conda: https://conda.anaconda.org/conda-forge/linux-aarch64/tk-8.6.13-noxft_h0dc03b3_103.conda - conda: https://conda.anaconda.org/conda-forge/noarch/tqdm-4.67.3-pyh8f84b5b_0.conda -- conda: https://conda.anaconda.org/conda-forge/noarch/typeguard-4.5.1-pyhd8ed1ab_0.conda +- conda: https://conda.anaconda.org/conda-forge/noarch/typeguard-4.5.2-pyhcf101f3_0.conda - conda: https://conda.anaconda.org/conda-forge/noarch/typing-extensions-4.15.0-h396c80c_0.conda -- conda: https://conda.anaconda.org/conda-forge/noarch/typing-inspection-0.4.2-pyhd8ed1ab_1.conda +- conda: https://conda.anaconda.org/conda-forge/noarch/typing-inspection-0.4.2-pyhcf101f3_2.conda - conda: https://conda.anaconda.org/conda-forge/noarch/typing_extensions-4.15.0-pyhcf101f3_0.conda - conda: https://conda.anaconda.org/conda-forge/noarch/tzdata-2025c-hc9c84f9_1.conda -- conda: https://conda.anaconda.org/conda-forge/noarch/urllib3-2.6.3-pyhd8ed1ab_0.conda +- conda: https://conda.anaconda.org/conda-forge/noarch/urllib3-2.7.0-pyhd8ed1ab_0.conda - conda: https://conda.anaconda.org/conda-forge/linux-aarch64/xorg-libxau-1.0.12-he30d5cf_1.conda - conda: https://conda.anaconda.org/conda-forge/linux-aarch64/xorg-libxdmcp-1.1.5-he30d5cf_1.conda - conda: https://conda.anaconda.org/conda-forge/linux-aarch64/yaml-0.2.5-h80f16a2_3.conda -- conda: https://conda.anaconda.org/conda-forge/noarch/zipp-3.23.0-pyhcf101f3_1.conda +- conda: https://conda.anaconda.org/conda-forge/noarch/zipp-4.1.0-pyhcf101f3_0.conda - conda: https://conda.anaconda.org/conda-forge/linux-aarch64/zlib-ng-2.3.3-ha7cb516_1.conda - conda: https://conda.anaconda.org/conda-forge/linux-aarch64/zstd-1.5.7-h85ac4a6_6.conda packages: @@ -173,15 +170,15 @@ license: MIT license_family: MIT size: 64927 timestamp: 1773935801332 -- conda: https://conda.anaconda.org/conda-forge/noarch/backports.zstd-1.3.0-py314h680f03e_0.conda +- conda: https://conda.anaconda.org/conda-forge/noarch/backports.zstd-1.5.0-py314h680f03e_0.conda noarch: generic -sha256: c31ab719d256bc6f89926131e88ecd0f0c5d003fe8481852c6424f4ec6c7eb29 -md5: a2ac7763a9ac75055b68f325d3255265 +sha256: a1c97297e867776760489537bc5ae36fa83a154be30e3b79385a39ca4cb058fe +md5: 1133126d840e75287d83947be3fc3e71 depends: - python >=3.14 license: BSD-3-Clause AND MIT AND EPL-2.0 -size: 7514 -timestamp: 1767044983590 +size: 7533 +timestamp: 1778594057496 - conda: https://conda.anaconda.org/conda-forge/linux-aarch64/brotli-python-1.2.0-py314h352cb57_1.conda sha256: 5a5b0cdcd7ed89c6a8fb830924967f6314a2b71944bc1ebc2c105781ba97aa75 md5: a1b5c571a0923a205d663d8678df4792 @@ -206,42 +203,41 @@ license: bzip2-1.0.6 license_family: BSD size: 192412 timestamp: 1771350241232 -- conda: https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2026.2.25-hbd8a1cb_0.conda -sha256: 67cc7101b36421c5913a1687ef1b99f85b5d6868da3abbf6ec1a4181e79782fc -md5: 4492fd26db29495f0ba23f146cd5638d +- conda: https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2026.4.22-hbd8a1cb_0.conda +sha256: c9dbcc8039a52023660d6d1bbf87594a93dd69c6ac5a2a44323af2c92976728d +md5: e18ad67cf881dcadee8b8d9e2f8e5f73 depends: - __unix license: ISC -size: 147413 -timestamp: 1772006283803 -- conda: https://conda.anaconda.org/conda-forge/noarch/certifi-2026.2.25-pyhd8ed1ab_0.conda -sha256: a6b118fd1ed6099dc4fc03f9c492b88882a780fadaef4ed4f93dc70757713656 -md5: 765c4d97e877cdbbb88ff33152b86125 +size: 131039 +timestamp: 1776865545798 +- conda: https://conda.anaconda.org/conda-forge/noarch/certifi-2026.4.22-pyhd8ed1ab_0.conda +sha256: 989db6e5957c4b44fa600c68c681ec2f36a55e48f7c7f1c073d5e91caa8cd878 +md5: 929471569c93acefb30282a22060dcd5 depends: - python >=3.10 license: ISC -size: 151445 -timestamp: 1772001170301 -- conda: https://conda.anaconda.org/conda-forge/noarch/charset-normalizer-3.4.6-pyhd8ed1ab_0.conda -sha256: d86dfd428b2e3c364fa90e07437c8405d635aa4ef54b25ab51d9c712be4112a5 -md5: 49ee13eb9b8f44d63879c69b8a40a74b +size: 135656 +timestamp: 1776866680878 +- conda: https://conda.anaconda.org/conda-forge/noarch/charset-normalizer-3.4.7-pyhd8ed1ab_0.conda +sha256: 3f9483d62ce24ecd063f8a5a714448445dc8d9e201147c46699fc0033e824457 +md5: a9167b9571f3baa9d448faa2139d1089 depends: - python >=3.10 license: MIT license_family: MIT -size: 58510 -timestamp: 1773660086450 -- conda: https://conda.anaconda.org/conda-forge/noarch/click-8.3.1-pyh8f84b5b_1.conda -sha256: 38cfe1ee75b21a8361c8824f5544c3866f303af1762693a178266d7f198e8715 -md5: ea8a6c3256897cc31263de9f455e25d9 +size: 58872 +timestamp: 1775127203018 +- conda: https://conda.anaconda.org/conda-forge/noarch/click-8.4.0-pyhc90fa1f_0.conda +sha256: 99ab8ef815c4520cce3a7482c2513f377c14348206857661d84c76a55e030f97 +md5: 003767c47f1f0a474c4de268b57839c3 depends: -- python >=3.10 - __unix - python +- python >=3.10 license: BSD-3-Clause -license_family: BSD -size: 97676 -timestamp: 1764518652276 +size: 104631 +timestamp: 1779108494556 - conda: https://conda.anaconda.org/conda-forge/noarch/coloredlogs-15.0.1-pyhd8ed1ab_4.conda sha256: 8021c76eeadbdd5784b881b165242db9449783e12ce26d6234060026fd6a8680 md5: b866ff7007b934d564961066c8195983 @@ -263,26 +259,26 @@ license: BSD-3-Clause license_family: BSD size: 39326 timestamp: 1735759976140 -- conda: https://conda.anaconda.org/conda-forge/noarch/cpython-3.14.3-py314hd8ed1ab_101.conda +- conda: https://conda.anaconda.org/conda-forge/noarch/cpython-3.14.4-py314hd8ed1ab_100.conda noarch: generic -sha256: 91b06300879df746214f7363d6c27c2489c80732e46a369eb2afc234bcafb44c -md5: 3bb89e4f795e5414addaa531d6b1500a +sha256: 40dc224f2b718e5f034efd2332bc315a719063235f63673468d26a24770094ee +md5: f111d4cfaf1fe9496f386bc98ae94452 depends: - python >=3.14,<3.15.0a0 - python_abi * *_cp314 license: Python-2.0 -size: 50078 -timestamp: 1770674447292 -- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/expat-2.7.4-hfae3067_0.conda -sha256: 5f087bef054c681edcaae84a8c2230585b938691e371ff92957a30707b7fcdf7 -md5: b304307db639831ad7caabd2eac6fca6 +size: 49809 +timestamp: 1775614256655 +- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/expat-2.8.0-hfae3067_0.conda +sha256: f9eebe138dfa9693bfeab5fb7eac012474fa6dc8aaccd62d23b648b360db1bff +md5: 424b4cda90c1fa95f2d027f76d5ef97f depends: -- libexpat 2.7.4 hfae3067_0 +- libexpat 2.8.0 hfae3067_0 - libgcc >=14 license: MIT license_family: MIT -size: 137701 -timestamp: 1771259543650 +size: 140559 +timestamp: 1777846104900 - conda: https://conda.anaconda.org/conda-forge/noarch/font-ttf-dejavu-sans-mono-2.37-hab24e00_0.tar.bz2 sha256: 58d7f40d2940dd0a8aa28651239adbf5613254df0f75789919c4e6762054403b md5: 0c96522c6bdaed4b1566d11387caaf45 @@ -386,25 +382,16 @@ license: MIT license_family: MIT size: 17397 timestamp: 1737618427549 -- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/icu-78.3-hcab7f73_0.conda -sha256: 49ba6aed2c6b482bb0ba41078057555d29764299bc947b990708617712ef6406 -md5: 546da38c2fa9efacf203e2ad3f987c59 -depends: -- libgcc >=14 -- libstdcxx >=14 -license: MIT -license_family: MIT -size: 12837286 -timestamp: 1773822650615 -- conda: https://conda.anaconda.org/conda-forge/noarch/idna-3.11-pyhd8ed1ab_0.conda -sha256: ae89d0299ada2a3162c2614a9d26557a92aa6a77120ce142f8e0109bbf0342b0 -md5: 53abe63df7e10a6ba605dc5f9f961d36 +- conda: https://conda.anaconda.org/conda-forge/noarch/idna-3.13-pyhcf101f3_0.conda +sha256: 9ab620e6f64bb67737bd7bc1ad6f480770124e304c6710617aba7fe60b089f48 +md5: fb7130c190f9b4ec91219840a05ba3ac depends: - python >=3.10 +- python license: BSD-3-Clause license_family: BSD -size: 50721 -timestamp: 1760286526795 +size: 59038 +timestamp: 1776947141407 - conda: https://conda.anaconda.org/conda-forge/noarch/importlib-metadata-8.8.0-pyhcf101f3_0.conda sha256: 82ab2a0d91ca1e7e63ab6a4939356667ef683905dea631bc2121aa534d347b16 md5: 080594bf4493e6bae2607e65390c520a @@ -469,17 +456,17 @@ license: MIT license_family: MIT size: 65750397 timestamp: 1615199465742 -- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/lcms2-2.18-h9d5b58d_0.conda -sha256: 379ef5e91a587137391a6149755d0e929f1a007d2dcb211318ac670a46c8596f -md5: bb960f01525b5e001608afef9d47b79c +- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/lcms2-2.19.1-h9d5b58d_0.conda +sha256: 1e5f68e4b36a0e1a278c6dc026bc3d7775518a15832cbc9d7fc1c0e4c47784b1 +md5: b1f8bee3c53a6d2c103fb4a1ae44f5c4 depends: - libgcc >=14 -- libjpeg-turbo >=3.1.2,<4.0a0 +- libjpeg-turbo >=3.1.4.1,<4.0a0 - libtiff >=4.7.1,<4.8.0a0 license: MIT license_family: MIT -size: 293039 -timestamp: 1768184778398 +size: 296899 +timestamp: 1778079402392 - conda: https://conda.anaconda.org/conda-forge/linux-aarch64/ld_impl_linux-aarch64-2.45.1-default_h1979696_102.conda sha256: 7abd913d81a9bf00abb699e8987966baa2065f5132e37e815f92d90fc6bba530 md5: a21644fc4a83da26452a718dc9468d5f @@ -501,37 +488,37 @@ license: Apache-2.0 license_family: Apache size: 240444 timestamp: 1773114901155 -- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/libblas-3.11.0-5_haddc8a3_openblas.conda -build_number: 5 -sha256: 700f3c03d0fba8e687a345404a45fbabe781c1cf92242382f62cef2948745ec4 -md5: 5afcea37a46f76ec1322943b3c4dfdc0 +- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/libblas-3.11.0-7_haddc8a3_openblas.conda +build_number: 7 +sha256: f27ba323c2f1e1731b5e880fe520f178f55047f25be94f77e649605b2343c066 +md5: e8d07b777f6ff1fab69665336561910b depends: -- libopenblas >=0.3.30,<0.3.31.0a0 -- libopenblas >=0.3.30,<1.0a0 +- libopenblas >=0.3.33,<0.3.34.0a0 +- libopenblas >=0.3.33,<1.0a0 constrains: -- mkl <2026 -- libcblas 3.11.0 5*_openblas -- liblapack 3.11.0 5*_openblas -- liblapacke 3.11.0 5*_openblas -- blas 2.305 openblas +- liblapack 3.11.0 7*_openblas +- libcblas 3.11.0 7*_openblas +- mkl <2027 +- blas 2.307 openblas +- liblapacke 3.11.0 7*_openblas license: BSD-3-Clause license_family: BSD -size: 18369 -timestamp: 1765818610617 -- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/libcblas-3.11.0-5_hd72aa62_openblas.conda -build_number: 5 -sha256: 3fad5c9de161dccb4e42c8b1ae8eccb33f4ed56bccbcced9cbb0956ae7869e61 -md5: 0b2f1143ae2d0aa4c991959d0daaf256 -depends: -- libblas 3.11.0 5_haddc8a3_openblas +size: 18696 +timestamp: 1778489796402 +- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/libcblas-3.11.0-7_hd72aa62_openblas.conda +build_number: 7 +sha256: c8f0192362966df0828419f042d6f94c079e5df00ad6bd05b5e84c12b42f8cc7 +md5: 90ac57b82c055faa9be25031864b7d8f +depends: +- libblas 3.11.0 7_haddc8a3_openblas constrains: -- liblapack 3.11.0 5*_openblas -- liblapacke 3.11.0 5*_openblas -- blas 2.305 openblas +- liblapack 3.11.0 7*_openblas +- blas 2.307 openblas +- liblapacke 3.11.0 7*_openblas license: BSD-3-Clause license_family: BSD -size: 18371 -timestamp: 1765818618899 +size: 18664 +timestamp: 1778489802790 - conda: https://conda.anaconda.org/conda-forge/linux-aarch64/libdeflate-1.25-h1af38f5_0.conda sha256: 48814b73bd462da6eed2e697e30c060ae16af21e9fbed30d64feaf0aad9da392 md5: a9138815598fe6b91a1d6782ca657b0c @@ -541,17 +528,17 @@ license: MIT license_family: MIT size: 71117 timestamp: 1761979776756 -- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/libexpat-2.7.4-hfae3067_0.conda -sha256: 995ce3ad96d0f4b5ed6296b051a0d7b6377718f325bc0e792fbb96b0e369dad7 -md5: 57f3b3da02a50a1be2a6fe847515417d +- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/libexpat-2.8.0-hfae3067_0.conda +sha256: 206c422a7f4b462d1dc17d558f0299088d0992bd3309ae83f5440fcc4f130602 +md5: 3bacd6171f0a3f8fddd06c3d5ae01955 depends: - libgcc >=14 constrains: -- expat 2.7.4.* +- expat 2.8.0.* license: MIT license_family: MIT -size: 76564 -timestamp: 1771259530958 +size: 76996 +timestamp: 1777846096032 - conda: https://conda.anaconda.org/conda-forge/linux-aarch64/libffi-3.5.2-h376a255_0.conda sha256: 3df4c539449aabc3443bbe8c492c01d401eea894603087fca2917aa4e1c2dea9 md5: 2f364feefb6a7c00423e80dcb12db62a @@ -581,90 +568,90 @@ constrains: license: GPL-2.0-only OR FTL size: 422941 timestamp: 1774301093473 -- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/libgcc-15.2.0-h8acb6b2_18.conda -sha256: 43df385bedc1cab11993c4369e1f3b04b4ca5d0ea16cba6a0e7f18dbc129fcc9 -md5: 552567ea2b61e3a3035759b2fdb3f9a6 +- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/libgcc-15.2.0-h8acb6b2_19.conda +sha256: 4592b096e553f67799ae70d4b6167eeda3ec74587d68c7aecbf4e7b1df136681 +md5: f35b3f52d0a2ec4ffe3c89ba135cdb9a depends: - _openmp_mutex >=4.5 constrains: -- libgcc-ng ==15.2.0=*_18 -- libgomp 15.2.0 h8acb6b2_18 +- libgomp 15.2.0 h8acb6b2_19 +- libgcc-ng ==15.2.0=*_19 license: GPL-3.0-only WITH GCC-exception-3.1 license_family: GPL -size: 622900 -timestamp: 1771378128706 -- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/libgcc-ng-15.2.0-he9431aa_18.conda -sha256: 83bb0415f59634dccfa8335d4163d1f6db00a27b36666736f9842b650b92cf2f -md5: 4feebd0fbf61075a1a9c2e9b3936c257 +size: 622462 +timestamp: 1778268755949 +- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/libgcc-ng-15.2.0-he9431aa_19.conda +sha256: 1137f93f477f56199ded24117430045a0c02cbe8b10031beac3b9ad2138539d3 +md5: 770cf892e5530f43e63cadc673e85653 depends: -- libgcc 15.2.0 h8acb6b2_18 +- libgcc 15.2.0 h8acb6b2_19 license: GPL-3.0-only WITH GCC-exception-3.1 license_family: GPL -size: 27568 -timestamp: 1771378136019 -- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/libgfortran-15.2.0-he9431aa_18.conda -sha256: 7dcd7dff2505d56fd5272a6e712ec912f50a46bf07dc6873a7e853694304e6e4 -md5: 41f261f5e4e2e8cbd236c2f1f15dae1b +size: 27738 +timestamp: 1778268759211 +- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/libgfortran-15.2.0-he9431aa_19.conda +sha256: e5ad94be72634233510b33ba792a3339921bd468f0b8bc6961ea05eded251d9b +md5: c7a5b5decf969ead5ecada83654164cf depends: -- libgfortran5 15.2.0 h1b7bec0_18 +- libgfortran5 15.2.0 h1b7bec0_19 constrains: -- libgfortran-ng ==15.2.0=*_18 +- libgfortran-ng ==15.2.0=*_19 license: GPL-3.0-only WITH GCC-exception-3.1 license_family: GPL -size: 27587 -timestamp: 1771378169244 -- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/libgfortran5-15.2.0-h1b7bec0_18.conda -sha256: 85347670dfb4a8d4c13cd7cae54138dcf2b1606b6bede42eef5507bf5f9660c6 -md5: 574d88ce3348331e962cfa5ed451b247 +size: 27728 +timestamp: 1778268784621 +- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/libgfortran5-15.2.0-h1b7bec0_19.conda +sha256: af8e9bdcaa77f133a8ee4c1ef57ef564d9c45aa262abf9f5ef9b50eb99d96407 +md5: 779dbb494de6d3d6477cab52eb34285a depends: - libgcc >=15.2.0 constrains: - libgfortran 15.2.0 license: GPL-3.0-only WITH GCC-exception-3.1 license_family: GPL -size: 1486341 -timestamp: 1771378148102 -- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/libgomp-15.2.0-h8acb6b2_18.conda -sha256: fc716f11a6a8525e27a5d332ef6a689210b0d2a4dd1133edc0f530659aa9faa6 -md5: 4faa39bf919939602e594253bd673958 +size: 1487244 +timestamp: 1778268767295 +- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/libgomp-15.2.0-h8acb6b2_19.conda +sha256: 2370ef0ffcbae5bede3c4bf136add4abc257245eb91f724c99bb4a43116c5a83 +md5: c5e8a379c4a2ec2aea4ba22758c001d9 license: GPL-3.0-only WITH GCC-exception-3.1 license_family: GPL -size: 588060 -timestamp: 1771378040807 -- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/libjpeg-turbo-3.1.2-he30d5cf_0.conda -sha256: 84064c7c53a64291a585d7215fe95ec42df74203a5bf7615d33d49a3b0f08bb6 -md5: 5109d7f837a3dfdf5c60f60e311b041f +size: 587387 +timestamp: 1778268674393 +- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/libjpeg-turbo-3.1.4.1-he30d5cf_0.conda +sha256: e97ec2af5f09f8f6ea8ecd550055c95ae80fae22015fcfadaa94eafe025c9ccc +md5: a85ba48648f6868016f2741fd9170250 depends: - libgcc >=14 constrains: - jpeg <0.0.0a license: IJG AND BSD-3-Clause AND Zlib -size: 691818 -timestamp: 1762094728337 -- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/liblapack-3.11.0-5_h88aeb00_openblas.conda -build_number: 5 -sha256: 692222d186d3ffbc99eaf04b5b20181fd26aee1edec1106435a0a755c57cce86 -md5: 88d1e4133d1182522b403e9ba7435f04 -depends: -- libblas 3.11.0 5_haddc8a3_openblas +size: 693143 +timestamp: 1775962625956 +- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/liblapack-3.11.0-7_h88aeb00_openblas.conda +build_number: 7 +sha256: 20b38a0156200ac65f597bf0a93914c565435f2cc58b1042581854231a99ac35 +md5: 5899cbd743cc74fd655c1ed2af7120f3 +depends: +- libblas 3.11.0 7_haddc8a3_openblas constrains: -- liblapacke 3.11.0 5*_openblas -- blas 2.305 openblas -- libcblas 3.11.0 5*_openblas +- libcblas 3.11.0 7*_openblas +- blas 2.307 openblas +- liblapacke 3.11.0 7*_openblas license: BSD-3-Clause license_family: BSD -size: 18392 -timestamp: 1765818627104 -- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/liblzma-5.8.2-he30d5cf_0.conda -sha256: 843c46e20519651a3e357a8928352b16c5b94f4cd3d5481acc48be2e93e8f6a3 -md5: 96944e3c92386a12755b94619bae0b35 +size: 18685 +timestamp: 1778489809140 +- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/liblzma-5.8.3-he30d5cf_0.conda +sha256: d61962b9cd54c3554361550203c64d5b65b71e3058a285b66e4b04b9769f0a5c +md5: 76298a9e6d71ee6e832a8d0d7373b261 depends: - libgcc >=14 constrains: -- xz 5.8.2.* +- xz 5.8.3.* license: 0BSD -size: 125916 -timestamp: 1768754941722 +size: 126102 +timestamp: 1775828008518 - conda: https://conda.anaconda.org/conda-forge/linux-aarch64/libmpdec-4.0.0-he30d5cf_1.conda sha256: 57c0dd12d506e84541c4e877898bd2a59cca141df493d34036f18b2751e0a453 md5: 7b9813e885482e3ccb1fa212b86d7fd0 @@ -674,49 +661,48 @@ license: BSD-2-Clause license_family: BSD size: 114056 timestamp: 1769482343003 -- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/libopenblas-0.3.30-pthreads_h9d3fd7e_4.conda -sha256: 794a7270ea049ec931537874cd8d2de0ef4b3cef71c055cfd8b4be6d2f4228b0 -md5: 11d7d57b7bdd01da745bbf2b67020b2e +- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/libopenblas-0.3.33-pthreads_h9d3fd7e_0.conda +sha256: b018ecfb05e75a8eea3f21f6b5c5c2a54b5178bdcf19e2e2df2735740214a8c8 +md5: 58a66cd95e9692f08abe89f55a6f3f12 depends: - libgcc >=14 - libgfortran - libgfortran5 >=14.3.0 constrains: -- openblas >=0.3.30,<0.3.31.0a0 +- openblas >=0.3.33,<0.3.34.0a0 license: BSD-3-Clause license_family: BSD -size: 4959359 -timestamp: 1763114173544 -- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/libpng-1.6.55-h1abf092_0.conda -sha256: c7378c6b79de4d571d00ad1caf0a4c19d43c9c94077a761abb6ead44d891f907 -md5: be4088903b94ea297975689b3c3aeb27 +size: 5121336 +timestamp: 1776993423004 +- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/libpng-1.6.58-h1abf092_0.conda +sha256: 483eaa53da40a6a3e558709d9f7b1ca388735364ae21a1ba58cf942514649c92 +md5: f51503ac45a4888bce71af9027a2ecc9 depends: - libgcc >=14 -- libzlib >=1.3.1,<2.0a0 +- libzlib >=1.3.2,<2.0a0 license: zlib-acknowledgement -size: 340156 -timestamp: 1770691477245 -- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/libsqlite-3.52.0-h10b116e_0.conda -sha256: 1ddaf91b44fae83856276f4cb7ce544ffe41d4b55c1e346b504c6b45f19098d6 -md5: 77891484f18eca74b8ad83694da9815e +size: 341202 +timestamp: 1776315188425 +- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/libsqlite-3.53.1-h022381a_0.conda +sha256: ad03b7d8e4d08001f0df88ee7a56108bb35bae4795a42b9a04cc1abfa822bd07 +md5: 2ec1119217d8f0d086e9a62f3cb0e5ea depends: -- icu >=78.2,<79.0a0 - libgcc >=14 -- libzlib >=1.3.1,<2.0a0 +- libzlib >=1.3.2,<2.0a0 license: blessing -size: 952296 -timestamp: 1772818881550 -- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/libstdcxx-15.2.0-hef695bb_18.conda -sha256: 31fdb9ffafad106a213192d8319b9f810e05abca9c5436b60e507afb35a6bc40 -md5: f56573d05e3b735cb03efeb64a15f388 +size: 955361 +timestamp: 1777986487553 +- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/libstdcxx-15.2.0-hef695bb_19.conda +sha256: 1dadc45e599f510dd5f97141dddcdbb9844d9f1430c1f3a38075cf1c58f87b4e +md5: 543fbc8d71f2a0baf04cf88ce96cb8bb depends: -- libgcc 15.2.0 h8acb6b2_18 +- libgcc 15.2.0 h8acb6b2_19 constrains: -- libstdcxx-ng ==15.2.0=*_18 +- libstdcxx-ng ==15.2.0=*_19 license: GPL-3.0-only WITH GCC-exception-3.1 license_family: GPL -size: 5541411 -timestamp: 1771378162499 +size: 5546559 +timestamp: 1778268777463 - conda: https://conda.anaconda.org/conda-forge/linux-aarch64/libtiff-4.7.1-hdb009f0_1.conda sha256: 7ff79470db39e803e21b8185bc8f19c460666d5557b1378d1b1e857d929c6b39 md5: 8c6fd84f9c87ac00636007c6131e457d @@ -733,15 +719,14 @@ depends: license: HPND size: 488407 timestamp: 1762022048105 -- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/libuuid-2.41.3-h1022ec0_0.conda -sha256: c37a8e89b700646f3252608f8368e7eb8e2a44886b92776e57ad7601fc402a11 -md5: cf2861212053d05f27ec49c3784ff8bb +- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/libuuid-2.42.1-h1022ec0_0.conda +sha256: 1628839b062e98b2192857d4da8496ac9ac6b0dbb77aa040c34efc9192c440ee +md5: 0f42f9fedd2a32d798de95a7f65c456f depends: - libgcc >=14 license: BSD-3-Clause -license_family: BSD size: 43453 -timestamp: 1766271546875 +timestamp: 1779118526838 - conda: https://conda.anaconda.org/conda-forge/linux-aarch64/libwebp-base-1.6.0-ha2e29f5_0.conda sha256: b03700a1f741554e8e5712f9b06dd67e76f5301292958cd3cb1ac8c6fdd9ed25 md5: 24e92d0942c799db387f5c9d7b81f1af @@ -785,16 +770,16 @@ license: BSD-3-Clause license_family: BSD size: 85893 timestamp: 1770694658918 -- conda: https://conda.anaconda.org/conda-forge/noarch/markdown-it-py-4.0.0-pyhd8ed1ab_0.conda -sha256: 7b1da4b5c40385791dbc3cc85ceea9fad5da680a27d5d3cb8bfaa185e304a89e -md5: 5b5203189eb668f042ac2b0826244964 +- conda: https://conda.anaconda.org/conda-forge/noarch/markdown-it-py-4.2.0-pyhd8ed1ab_0.conda +sha256: 0c4c35376fe920714390d46e4b8d31c876d65f18e1655899e0763ec25f2a902f +md5: 6d03368f2b2b0a5fb6839df53b2eb5e0 depends: - mdurl >=0.1,<1 - python >=3.10 license: MIT license_family: MIT -size: 64736 -timestamp: 1754951288511 +size: 69017 +timestamp: 1778169663339 - conda: https://conda.anaconda.org/conda-forge/linux-aarch64/markupsafe-3.0.3-py314hb76de3f_1.conda sha256: 383c188496d13a55658c06e61e7d4cdff2c9f9d5a0648769fca8250bece7e0ef md5: e5de3c36dd548b35ff2a8aa49208dcb3 @@ -824,9 +809,9 @@ license: MIT license_family: MIT size: 14465 timestamp: 1733255681319 -- conda: https://conda.anaconda.org/bioconda/noarch/multiqc-1.33-pyhdfd78af_0.conda -sha256: f005760b13093362fc9c997d603dd487de32ab2e821a3cbce52a42bcb8136517 -md5: 698a8a27c2b9d8a542c70cb47099a75e +- conda: https://conda.anaconda.org/bioconda/noarch/multiqc-1.35-pyhdfd78af_0.conda +sha256: 5267ddcc9119b8bdfdddd83fa4713edf6e956443f7369ebd686dc6d9f921a428 +md5: d95457757ad503af93145630ec6e8965 depends: - click - coloredlogs @@ -840,10 +825,10 @@ depends: - packaging - pillow >=10.2.0 - plotly >=5.18 -- polars-lts-cpu +- polars >=1.34.0 - pyaml-env - pydantic >=2.7.1 -- python >=3.8,!=3.14.1 +- python >=3.9,!=3.14.1 - python-dotenv - python-kaleido 0.2.1 - pyyaml >=4 @@ -853,20 +838,21 @@ depends: - spectra >=0.0.10 - tiktoken - tqdm -- typeguard +- typeguard >=4 license: GPL-3.0-or-later license_family: GPL3 -size: 4198799 -timestamp: 1765300743879 -- conda: https://conda.anaconda.org/conda-forge/noarch/narwhals-2.18.1-pyhcf101f3_1.conda -sha256: 541fd4390a0687228b8578247f1536a821d9261389a65585af9d1a6f2a14e1e0 -md5: 30bec5e8f4c3969e2b1bd407c5e52afb +size: 4229065 +timestamp: 1778635617929 +- conda: https://conda.anaconda.org/conda-forge/noarch/narwhals-2.21.2-pyhcf101f3_0.conda +sha256: 70f43d62450927d51673eecd8823e14f5b3cfebdb43cda1d502eba97162bab42 +md5: 6687827c332121727ce383919e1ec8c2 depends: - python >=3.10 - python license: MIT -size: 280459 -timestamp: 1774380620329 +license_family: MIT +size: 284323 +timestamp: 1778929680962 - conda: https://conda.anaconda.org/conda-forge/noarch/natsort-8.4.0-pyhcf101f3_2.conda sha256: aeb1548eb72e4f198e72f19d242fb695b35add2ac7b2c00e0d83687052867680 md5: e941e85e273121222580723010bd4fa2 @@ -877,14 +863,14 @@ license: MIT license_family: MIT size: 39262 timestamp: 1770905275632 -- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/ncurses-6.5-ha32ae93_3.conda -sha256: 91cfb655a68b0353b2833521dc919188db3d8a7f4c64bea2c6a7557b24747468 -md5: 182afabe009dc78d8b73100255ee6868 +- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/ncurses-6.6-hf8d1292_0.conda +sha256: 369db85c5cd8d99dde364ce70725d76511d9c8199e5b820c740414091bf5bcca +md5: b2a43456aa56fe80c2477a5094899eff depends: -- libgcc >=13 +- libgcc >=14 license: X11 AND BSD-3-Clause -size: 926034 -timestamp: 1738196018799 +size: 960036 +timestamp: 1777422174534 - conda: https://conda.anaconda.org/conda-forge/noarch/networkx-3.6.1-pyhcf101f3_0.conda sha256: f6a82172afc50e54741f6f84527ef10424326611503c64e359e25a19a8e4c1c6 md5: a2c1eeadae7a309daed9d62c96012a2b @@ -923,24 +909,23 @@ license: MPL-2.0 license_family: MOZILLA size: 2061869 timestamp: 1763490303490 -- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/numpy-2.4.3-py314haac167e_0.conda -sha256: a6d42fd88afc57c3b0a57b21a12eff7492dfc419bb61ee3f74e9ba6261dabc88 -md5: 25d896c331481145720a21e5145fad65 +- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/numpy-2.4.5-py314he1698a1_0.conda +sha256: 84c4b05037cc1b73749c41977bc3e204b3f4a11cc750984b44d3462a6eb865a3 +md5: bdb49f3f231962d4bca98ed2c59ab92f depends: - python -- libgcc >=14 -- python 3.14.* *_cp314 - libstdcxx >=14 -- libcblas >=3.9.0,<4.0a0 +- libgcc >=14 +- libblas >=3.9.0,<4.0a0 - liblapack >=3.9.0,<4.0a0 - python_abi 3.14.* *_cp314 -- libblas >=3.9.0,<4.0a0 +- libcblas >=3.9.0,<4.0a0 constrains: - numpy-base <0a0 license: BSD-3-Clause license_family: BSD -size: 8008045 -timestamp: 1773839355275 +size: 8005231 +timestamp: 1778894364326 - conda: https://conda.anaconda.org/conda-forge/linux-aarch64/openjpeg-2.5.4-h5da879a_0.conda sha256: bd1bc8bdde5e6c5cbac42d462b939694e40b59be6d0698f668515908640c77b8 md5: cea962410e327262346d48d01f05936c @@ -954,47 +939,47 @@ license: BSD-2-Clause license_family: BSD size: 392636 timestamp: 1758489353577 -- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/openssl-3.6.1-h546c87b_1.conda -sha256: 7f8048c0e75b2620254218d72b4ae7f14136f1981c5eb555ef61645a9344505f -md5: 25f5885f11e8b1f075bccf4a2da91c60 +- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/openssl-3.6.2-h546c87b_0.conda +sha256: 348cb74c1530ac241215d047ef65d134cf797af935c97a68655319362b7e6a01 +md5: 3b129669089e4d6a5c6871dbb4669b99 depends: - ca-certificates - libgcc >=14 license: Apache-2.0 license_family: Apache -size: 3692030 -timestamp: 1769557678657 -- conda: https://conda.anaconda.org/conda-forge/noarch/packaging-26.0-pyhcf101f3_0.conda -sha256: c1fc0f953048f743385d31c468b4a678b3ad20caffdeaa94bed85ba63049fd58 -md5: b76541e68fea4d511b1ac46a28dcd2c6 +size: 3706406 +timestamp: 1775589602258 +- conda: https://conda.anaconda.org/conda-forge/noarch/packaging-26.2-pyhc364b38_0.conda +sha256: 3906abfb6511a3bb309e39b9b1b7bc38f50a723971de2395489fd1f379255890 +md5: 4c06a92e74452cfa53623a81592e8934 depends: - python >=3.8 - python license: Apache-2.0 license_family: APACHE -size: 72010 -timestamp: 1769093650580 -- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/pillow-12.1.1-py314hac3e5ec_0.conda -sha256: 1ca2d1616baad9bccb7ebc425ef2dcd6cebe742fbe91edf226fb606ad371ca0f -md5: d3c959c7efe560b2d7da459d69121fe9 +size: 91574 +timestamp: 1777103621679 +- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/pillow-12.2.0-py314hac3e5ec_0.conda +sha256: 96b26c2657275ffe84ab510edf0865e21999d791485d12794edd4a71b837beb6 +md5: 87d58d103b47c4a8567b3d7666647684 depends: - python -- python 3.14.* *_cp314 - libgcc >=14 -- zlib-ng >=2.3.3,<2.4.0a0 +- python 3.14.* *_cp314 +- openjpeg >=2.5.4,<3.0a0 +- libxcb >=1.17.0,<2.0a0 - libwebp-base >=1.6.0,<2.0a0 +- zlib-ng >=2.3.3,<2.4.0a0 +- python_abi 3.14.* *_cp314 +- lcms2 >=2.18,<3.0a0 - tk >=8.6.13,<8.7.0a0 -- libfreetype >=2.14.1 -- libfreetype6 >=2.14.1 - libtiff >=4.7.1,<4.8.0a0 -- lcms2 >=2.18,<3.0a0 -- python_abi 3.14.* *_cp314 -- openjpeg >=2.5.4,<3.0a0 - libjpeg-turbo >=3.1.2,<4.0a0 -- libxcb >=1.17.0,<2.0a0 +- libfreetype >=2.14.3 +- libfreetype6 >=2.14.3 license: HPND -size: 1051828 -timestamp: 1770794010335 +size: 1062080 +timestamp: 1775060067775 - conda: https://conda.anaconda.org/conda-forge/noarch/plotly-6.6.0-pyhd8ed1ab_0.conda sha256: c418d325359fc7a0074cea7f081ef1bce26e114d2da8a0154c5d27ecc87a08e7 md5: 3e9427ee186846052e81fadde8ebe96a @@ -1008,11 +993,11 @@ license: MIT license_family: MIT size: 5251872 timestamp: 1772628857717 -- conda: https://conda.anaconda.org/conda-forge/noarch/polars-1.39.3-pyh58ad624_1.conda -sha256: d332c2d5002fc440ae37ed9679ffc21b552f18d20232390005d1dd3bce0888d3 -md5: d5a4e013a30dd8dfde9ab39f45aaf9c1 +- conda: https://conda.anaconda.org/conda-forge/noarch/polars-1.40.1-pyh58ad624_1.conda +sha256: 83e37ede46e8e57d4785e804604a88fa02d6eac9a774cee40d49018f9da9ead1 +md5: bdbac766376390889b74216b70206af4 depends: -- polars-runtime-32 ==1.39.3 +- polars-runtime-32 ==1.40.1 - python >=3.10 - python constrains: @@ -1026,55 +1011,29 @@ constrains: - pyiceberg >=0.7.1 - altair >=5.4.0 - great_tables >=0.8.0 -- polars-runtime-32 ==1.39.3 -- polars-runtime-64 ==1.39.3 -- polars-runtime-compat ==1.39.3 -license: MIT -license_family: MIT -size: 533495 -timestamp: 1774207987966 -- conda: https://conda.anaconda.org/conda-forge/noarch/polars-lts-cpu-1.34.0.deprecated-hc364b38_0.conda -sha256: e466fb31f67ba9bde18deafeb34263ca5eb25807f39ead0e9d753a8e82c4c4f4 -md5: ef0340e75068ac8ff96462749b5c98e7 -depends: -- polars >=1.34.0 -- polars-runtime-compat >=1.34.0 +- polars-runtime-32 ==1.40.1 +- polars-runtime-64 ==1.40.1 +- polars-runtime-compat ==1.40.1 license: MIT license_family: MIT -size: 3902 -timestamp: 1760206808444 -- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/polars-runtime-32-1.39.3-py310hff09b76_1.conda +size: 539000 +timestamp: 1778779696741 +- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/polars-runtime-32-1.40.1-py310h32c7c23_1.conda noarch: python -sha256: c070be507c5a90df397a47ae0299660be437d5546d68f1bc0fa4402c9f07d59e -md5: 3c1a7c6b4ba8b9fb773ace9723f8a5db +sha256: 2d7a84c62957f87ad4727d7c012ac6a14a45080565112b60232d13129d1ee5aa +md5: 3d94d946f9619f549a0a325120165745 depends: - python -- libgcc >=14 - libstdcxx >=14 -- _python_abi3_support 1.* -- cpython >=3.10 -constrains: -- __glibc >=2.17 -license: MIT -license_family: MIT -size: 34785466 -timestamp: 1774207998285 -- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/polars-runtime-compat-1.39.3-py310hf00a4a2_1.conda -noarch: python -sha256: 683315f1a49e47ce72bf9462419733b40b588b2b3106552d95fd4cd994e174de -md5: dd3464e2132dc3a783e76e5078870c76 -depends: -- python - libgcc >=14 -- libstdcxx >=14 - _python_abi3_support 1.* - cpython >=3.10 constrains: - __glibc >=2.17 license: MIT license_family: MIT -size: 34652491 -timestamp: 1774207996879 +size: 38145061 +timestamp: 1778779658728 - conda: https://conda.anaconda.org/conda-forge/linux-aarch64/procps-ng-4.0.6-h1779866_0.conda sha256: e9cbcbc94e151ada3d6dc365380aaaf591f65012c16d9a2abaea4b9b90adc402 md5: ab7288cc39545556d1bc5e71ab2df9a9 @@ -1104,24 +1063,23 @@ license: MIT license_family: MIT size: 14645 timestamp: 1736766960536 -- conda: https://conda.anaconda.org/conda-forge/noarch/pydantic-2.12.5-pyhcf101f3_1.conda -sha256: 868569d9505b7fe246c880c11e2c44924d7613a8cdcc1f6ef85d5375e892f13d -md5: c3946ed24acdb28db1b5d63321dbca7d +- conda: https://conda.anaconda.org/conda-forge/noarch/pydantic-2.13.4-pyhcf101f3_0.conda +sha256: 69700e31165df070e9716315e042196aa92525dae5deb5107785847ab9f4189f +md5: 729843edafc0899b3348bd3f19525b9d depends: - typing-inspection >=0.4.2 - typing_extensions >=4.14.1 - python >=3.10 -- typing-extensions >=4.6.1 - annotated-types >=0.6.0 -- pydantic-core ==2.41.5 +- pydantic-core ==2.46.4 - python license: MIT license_family: MIT -size: 340482 -timestamp: 1764434463101 -- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/pydantic-core-2.41.5-py314h451b6cc_1.conda -sha256: f8acb2d03ebe80fed0032b9a989fc9acfb6735e3cd3f8c704b72728cb31868f6 -md5: 28f5027a1e04d67aa13fac1c5ba79693 +size: 346511 +timestamp: 1778103405862 +- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/pydantic-core-2.46.4-py314h451b6cc_0.conda +sha256: 1a7c6b18e404c13c4d959888ecb48a9ed9de0e41be2872932b83a35278088df0 +md5: 9c3ace6aba6df14b943256095ac1281e depends: - python - typing-extensions >=4.6.0,!=4.7.0 @@ -1132,17 +1090,17 @@ constrains: - __glibc >=2.17 license: MIT license_family: MIT -size: 1828339 -timestamp: 1762989038561 -- conda: https://conda.anaconda.org/conda-forge/noarch/pygments-2.19.2-pyhd8ed1ab_0.conda -sha256: 5577623b9f6685ece2697c6eb7511b4c9ac5fb607c9babc2646c811b428fd46a -md5: 6b6ece66ebcae2d5f326c77ef2c5a066 +size: 1780773 +timestamp: 1778084251775 +- conda: https://conda.anaconda.org/conda-forge/noarch/pygments-2.20.0-pyhd8ed1ab_0.conda +sha256: cf70b2f5ad9ae472b71235e5c8a736c9316df3705746de419b59d442e8348e86 +md5: 16c18772b340887160c79a6acc022db0 depends: -- python >=3.9 +- python >=3.10 license: BSD-2-Clause license_family: BSD -size: 889287 -timestamp: 1750615908735 +size: 893031 +timestamp: 1774796815820 - conda: https://conda.anaconda.org/conda-forge/noarch/pysocks-1.7.1-pyha55dd90_7.conda sha256: ba3b032fa52709ce0d9fd388f63d330a026754587a2f461117cac9ab73d8d0d8 md5: 461219d1a5bd61342293efa2c0c90eac @@ -1153,31 +1111,31 @@ license: BSD-3-Clause license_family: BSD size: 21085 timestamp: 1733217331982 -- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/python-3.14.3-hb06a95a_101_cp314.conda -build_number: 101 -sha256: 87e9dff5646aba87cecfbc08789634c855871a7325169299d749040b0923a356 -md5: 205011b36899ff0edf41b3db0eda5a44 +- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/python-3.14.4-hfd9ac0a_100_cp314.conda +build_number: 100 +sha256: d29da77f75e8f9184cc9502d5c44be87397291a9e88819d5418322a173f76303 +md5: 3cfbe780f0f51cc8cba41db9f8a28bfe depends: - bzip2 >=1.0.8,<2.0a0 - ld_impl_linux-aarch64 >=2.36.1 -- libexpat >=2.7.3,<3.0a0 +- libexpat >=2.7.5,<3.0a0 - libffi >=3.5.2,<3.6.0a0 - libgcc >=14 - liblzma >=5.8.2,<6.0a0 - libmpdec >=4.0.0,<5.0a0 -- libsqlite >=3.51.2,<4.0a0 -- libuuid >=2.41.3,<3.0a0 -- libzlib >=1.3.1,<2.0a0 +- libsqlite >=3.52.0,<4.0a0 +- libuuid >=2.42,<3.0a0 +- libzlib >=1.3.2,<2.0a0 - ncurses >=6.5,<7.0a0 -- openssl >=3.5.5,<4.0a0 +- openssl >=3.5.6,<4.0a0 - python_abi 3.14.* *_cp314 - readline >=8.3,<9.0a0 - tk >=8.6.13,<8.7.0a0 - tzdata - zstd >=1.5.7,<1.6.0a0 license: Python-2.0 -size: 37305578 -timestamp: 1770674395875 +size: 37409899 +timestamp: 1775613674766 python_site_packages_path: lib/python3.14/site-packages - conda: https://conda.anaconda.org/conda-forge/noarch/python-dotenv-1.2.2-pyhcf101f3_0.conda sha256: 74e417a768f59f02a242c25e7db0aa796627b5bc8c818863b57786072aeb85e5 @@ -1188,15 +1146,15 @@ license: BSD-3-Clause license_family: BSD size: 27848 timestamp: 1772388605021 -- conda: https://conda.anaconda.org/conda-forge/noarch/python-gil-3.14.3-h4df99d1_101.conda -sha256: 233aebd94c704ac112afefbb29cf4170b7bc606e22958906f2672081bc50638a -md5: 235765e4ea0d0301c75965985163b5a1 +- conda: https://conda.anaconda.org/conda-forge/noarch/python-gil-3.14.4-h4df99d1_100.conda +sha256: 36ff7984e4565c85149e64f8206303d412a0652e55cf806dcb856903fa056314 +md5: e4e60721757979d01d3964122f674959 depends: -- cpython 3.14.3.* +- cpython 3.14.4.* - python_abi * *_cp314 license: Python-2.0 -size: 50062 -timestamp: 1770674497152 +size: 49806 +timestamp: 1775614307464 - conda: https://conda.anaconda.org/conda-forge/noarch/python-kaleido-0.2.1-pyhd8ed1ab_0.tar.bz2 sha256: e17bf63a30aec33432f1ead86e15e9febde9fc40a7f869c0e766be8d2db44170 md5: 310259a5b03ff02289d7705f39e2b1d2 @@ -1253,9 +1211,9 @@ license: MIT license_family: MIT size: 51788 timestamp: 1760379115194 -- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/regex-2026.2.28-py314h51f160d_0.conda -sha256: 2080ecea825e1ef91a2422cc0bc63e85db9e38908ed17657fb8f41de7a6eee71 -md5: 818aa2c9f6b3c808da5e7be22a9a424c +- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/regex-2026.5.9-py314h51f160d_0.conda +sha256: 05ef55f09f31eabd0a205f6b065e13fc746675f41924620977692ef0ffe5aad8 +md5: 34ed7bc9febeca70f55b757ca09c354d depends: - libgcc >=14 - python >=3.14,<3.15.0a0 @@ -1263,27 +1221,27 @@ depends: - python_abi 3.14.* *_cp314 license: Apache-2.0 AND CNRI-Python license_family: PSF -size: 408097 -timestamp: 1772255205521 -- conda: https://conda.anaconda.org/conda-forge/noarch/requests-2.32.5-pyhcf101f3_1.conda -sha256: 7813c38b79ae549504b2c57b3f33394cea4f2ad083f0994d2045c2e24cb538c5 -md5: c65df89a0b2e321045a9e01d1337b182 +size: 409780 +timestamp: 1778374195988 +- conda: https://conda.anaconda.org/conda-forge/noarch/requests-2.34.2-pyhcf101f3_0.conda +sha256: 1715246b19c9f85ee022933b4845f2fc14ac9184981b7b7d9b728bec8e9588da +md5: 4a85203c1d80c1059086ae860836ffb9 depends: - python >=3.10 -- certifi >=2017.4.17 +- certifi >=2023.5.7 - charset-normalizer >=2,<4 - idna >=2.5,<4 -- urllib3 >=1.21.1,<3 +- urllib3 >=1.26,<3 - python constrains: -- chardet >=3.0.2,<6 +- chardet >=3.0.2,<8 license: Apache-2.0 license_family: APACHE -size: 63602 -timestamp: 1766926974520 -- conda: https://conda.anaconda.org/conda-forge/noarch/rich-14.3.3-pyhcf101f3_0.conda -sha256: b06ce84d6a10c266811a7d3adbfa1c11f13393b91cc6f8a5b468277d90be9590 -md5: 7a6289c50631d620652f5045a63eb573 +size: 68709 +timestamp: 1778851103479 +- conda: https://conda.anaconda.org/conda-forge/noarch/rich-15.0.0-pyhcf101f3_0.conda +sha256: 3d6ba2c0fcdac3196ba2f0615b4104e532525ffa1335b50a2878be5ff488814a +md5: 0242025a3c804966bf71aa04eee82f66 depends: - markdown-it-py >=2.2.0 - pygments >=2.13.0,<3.0.0 @@ -1292,8 +1250,8 @@ depends: - python license: MIT license_family: MIT -size: 208472 -timestamp: 1771572730357 +size: 208577 +timestamp: 1775991661559 - conda: https://conda.anaconda.org/conda-forge/noarch/rich-click-1.9.7-pyh8f84b5b_0.conda sha256: aa3fcb167321bae51998de2e94d199109c9024f25a5a063cb1c28d8f1af33436 md5: 0c20a8ebcddb24a45da89d5e917e6cb9 @@ -1331,19 +1289,18 @@ license: MIT license_family: MIT size: 22284 timestamp: 1735770589188 -- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/sqlite-3.52.0-hf1c7be2_0.conda -sha256: 4f8523f5341f0d9e1547085206c6c1f71f9fc7c277443ca363a8cf98add8fc01 -md5: d9634079df93a65ee045b3c75f35cae1 +- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/sqlite-3.53.1-he8854b5_0.conda +sha256: 27467e4bfb0681546f149718c33b806fec078185fbaa6a4d17d440bc8f56185c +md5: 46009bdca2315a99e0a3a7d0ba1af3b9 depends: -- icu >=78.2,<79.0a0 - libgcc >=14 -- libsqlite 3.52.0 h10b116e_0 -- libzlib >=1.3.1,<2.0a0 -- ncurses >=6.5,<7.0a0 +- libsqlite 3.53.1 h022381a_0 +- libzlib >=1.3.2,<2.0a0 +- ncurses >=6.6,<7.0a0 - readline >=8.3,<9.0a0 license: blessing -size: 209416 -timestamp: 1772818891689 +size: 209964 +timestamp: 1777986493350 - conda: https://conda.anaconda.org/conda-forge/linux-aarch64/tiktoken-0.12.0-py314h6a36e60_3.conda sha256: c1da41c79262b27efa168407cfecc47b20270e5fc071a8307f95a2c85fb94170 md5: 55bf7b559202236157b14323b40f19e6 @@ -1382,20 +1339,20 @@ depends: license: MPL-2.0 and MIT size: 94132 timestamp: 1770153424136 -- conda: https://conda.anaconda.org/conda-forge/noarch/typeguard-4.5.1-pyhd8ed1ab_0.conda -sha256: 39d8ae33c43cdb8f771373e149b0b4fae5a08960ac58dcca95b2f1642bb17448 -md5: 260af1b0a94f719de76b4e14094e9a3b +- conda: https://conda.anaconda.org/conda-forge/noarch/typeguard-4.5.2-pyhcf101f3_0.conda +sha256: 59d7851d32fddb5b510272e6557aa982edeb927d349648dac27f5bf01d18bb26 +md5: 4460f039b7dedf15f7df086446ca75ae depends: -- importlib-metadata >=3.6 -- python >=3.10 -- typing-extensions >=4.10.0 - typing_extensions >=4.14.0 +- python >=3.10 +- importlib-metadata >=3.6 +- python constrains: - pytest >=7 license: MIT license_family: MIT -size: 36838 -timestamp: 1771532971545 +size: 38297 +timestamp: 1778779291237 - conda: https://conda.anaconda.org/conda-forge/noarch/typing-extensions-4.15.0-h396c80c_0.conda sha256: 7c2df5721c742c2a47b2c8f960e718c930031663ac1174da67c1ed5999f7938c md5: edd329d7d3a4ab45dcf905899a7a6115 @@ -1405,16 +1362,17 @@ license: PSF-2.0 license_family: PSF size: 91383 timestamp: 1756220668932 -- conda: https://conda.anaconda.org/conda-forge/noarch/typing-inspection-0.4.2-pyhd8ed1ab_1.conda -sha256: 70db27de58a97aeb7ba7448366c9853f91b21137492e0b4430251a1870aa8ff4 -md5: a0a4a3035667fc34f29bfbd5c190baa6 +- conda: https://conda.anaconda.org/conda-forge/noarch/typing-inspection-0.4.2-pyhcf101f3_2.conda +sha256: 8b90d2f19f9458b8c58a55e1fcdc1d90c1603a847a47654d8a454549413ba60a +md5: 53f5409c5cfd6c5a66417d68e3f0a864 depends: - python >=3.10 - typing_extensions >=4.12.0 +- python license: MIT license_family: MIT -size: 18923 -timestamp: 1764158430324 +size: 20935 +timestamp: 1777105465795 - conda: https://conda.anaconda.org/conda-forge/noarch/typing_extensions-4.15.0-pyhcf101f3_0.conda sha256: 032271135bca55aeb156cee361c81350c6f3fb203f57d024d7e5a1fc9ef18731 md5: 0caa1af407ecff61170c9437a808404d @@ -1431,9 +1389,9 @@ md5: ad659d0a2b3e47e38d829aa8cad2d610 license: LicenseRef-Public-Domain size: 119135 timestamp: 1767016325805 -- conda: https://conda.anaconda.org/conda-forge/noarch/urllib3-2.6.3-pyhd8ed1ab_0.conda -sha256: af641ca7ab0c64525a96fd9ad3081b0f5bcf5d1cbb091afb3f6ed5a9eee6111a -md5: 9272daa869e03efe68833e3dc7a02130 +- conda: https://conda.anaconda.org/conda-forge/noarch/urllib3-2.7.0-pyhd8ed1ab_0.conda +sha256: feff959a816f7988a0893201aa9727bbb7ee1e9cec2c4f0428269b489eb93fb4 +md5: cbb88288f74dbe6ada1c6c7d0a97223e depends: - backports.zstd >=1.0.0 - brotli-python >=1.2.0 @@ -1442,8 +1400,8 @@ depends: - python >=3.10 license: MIT license_family: MIT -size: 103172 -timestamp: 1767817860341 +size: 103560 +timestamp: 1778188657149 - conda: https://conda.anaconda.org/conda-forge/linux-aarch64/xorg-libxau-1.0.12-he30d5cf_1.conda sha256: e9f6e931feeb2f40e1fdbafe41d3b665f1ab6cb39c5880a1fcf9f79a3f3c84a5 md5: 1c246e1105000c3660558459e2fd6d43 @@ -1471,16 +1429,16 @@ license: MIT license_family: MIT size: 88088 timestamp: 1753484092643 -- conda: https://conda.anaconda.org/conda-forge/noarch/zipp-3.23.0-pyhcf101f3_1.conda -sha256: b4533f7d9efc976511a73ef7d4a2473406d7f4c750884be8e8620b0ce70f4dae -md5: 30cd29cb87d819caead4d55184c1d115 +- conda: https://conda.anaconda.org/conda-forge/noarch/zipp-4.1.0-pyhcf101f3_0.conda +sha256: 210bd31c22bb88f5e2a167df24c95bb5f152b2ada7502f9b8c49d1f5366db423 +md5: ba3dcdc8584155c97c648ae9c044b7a3 depends: - python >=3.10 - python license: MIT license_family: MIT -size: 24194 -timestamp: 1764460141901 +size: 24190 +timestamp: 1779159948016 - conda: https://conda.anaconda.org/conda-forge/linux-aarch64/zlib-ng-2.3.3-ha7cb516_1.conda sha256: 638a3a41a4fbfed52d3c60c8ef5a3693b3f12a5b1a3f58fa29f5698d0a0702e2 md5: f731af71c723065d91b4c01bb822641b diff --git a/modules/nf-core/multiqc/environment.yml b/modules/nf-core/multiqc/environment.yml index 009874d4..7a970e2b 100644 --- a/modules/nf-core/multiqc/environment.yml +++ b/modules/nf-core/multiqc/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::multiqc=1.33 + - bioconda::multiqc=1.35 diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf index 5376aea1..4c593a97 100644 --- a/modules/nf-core/multiqc/main.nf +++ b/modules/nf-core/multiqc/main.nf @@ -3,9 +3,9 @@ process MULTIQC { label 'process_single' conda "${moduleDir}/environment.yml" - container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container - ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/34/34e733a9ae16a27e80fe00f863ea1479c96416017f24a907996126283e7ecd4d/data' - : 'community.wave.seqera.io/library/multiqc:1.33--ee7739d47738383b'}" + container "${workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/12/1297c0f5075c19486da167ebf1b6136907d6b5339697b87b29fda335221785b3/data' + : 'community.wave.seqera.io/library/multiqc:1.35--839587b417d23042'}" 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 57cf43ca..b85d0e35 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-c1f4a7982b743963_1.txt + lock_file: modules/nf-core/multiqc/.conda-lock/linux_amd64-bd-839587b417d23042_1.txt linux/arm64: - lock_file: modules/nf-core/multiqc/.conda-lock/linux_arm64-bd-40bf3b435e89dc22_1.txt + lock_file: modules/nf-core/multiqc/.conda-lock/linux_arm64-bd-3e45d17b40a576b4_1.txt docker: linux/amd64: - name: community.wave.seqera.io/library/multiqc:1.33--c1f4a7982b743963 - build_id: bd-c1f4a7982b743963_1 - scan_id: sc-b7b7f470b2a16699_1 + name: community.wave.seqera.io/library/multiqc:1.35--839587b417d23042 + build_id: bd-839587b417d23042_1 + scan_id: sc-f87d7a31551c029f_1 linux/arm64: - name: community.wave.seqera.io/library/multiqc:1.33--40bf3b435e89dc22 - build_id: bd-40bf3b435e89dc22_1 - scan_id: sc-0e2108a0e7368d2f_1 + name: community.wave.seqera.io/library/multiqc:1.35--3e45d17b40a576b4 + build_id: bd-3e45d17b40a576b4_1 + scan_id: sc-1d0cf4ed1a4b61e0_1 singularity: linux/amd64: - name: oras://community.wave.seqera.io/library/multiqc:1.33--9b3473b1c4bb0493 - build_id: bd-9b3473b1c4bb0493_1 - https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/c4/c4e6d9f669e1a99b53c7dc5cdd6b8e7fd6654032c755bb783cc9849e8203f4d1/data + name: oras://community.wave.seqera.io/library/multiqc:1.35--cb7458fda84d6393 + build_id: bd-cb7458fda84d6393_1 + https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/12/1297c0f5075c19486da167ebf1b6136907d6b5339697b87b29fda335221785b3/data linux/arm64: - name: oras://community.wave.seqera.io/library/multiqc:1.33--e1ef2065eb21b530 - build_id: bd-e1ef2065eb21b530_1 - https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/2a/2acce766e3efb280fa43acdbe85305ea6496ddadbcaa2d806ac4985dfe4686ce/data + name: oras://community.wave.seqera.io/library/multiqc:1.35--f79e87603d312ac0 + build_id: bd-f79e87603d312ac0_1 + https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/c0/c007304153702edc622f1a76b41505e7fca65c7145e5b8b2ddce62a5c59af207/data diff --git a/modules/nf-core/multiqc/tests/main.nf.test.snap b/modules/nf-core/multiqc/tests/main.nf.test.snap index 3bfc524f..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", - "1.33" + "1.35" ] ] } @@ -175,7 +175,7 @@ [ "MULTIQC", "multiqc", - "1.33" + "1.35" ] ] } @@ -221,7 +221,7 @@ [ "MULTIQC", "multiqc", - "1.33" + "1.35" ] ] } @@ -314,7 +314,7 @@ [ "MULTIQC", "multiqc", - "1.33" + "1.35" ] ] } @@ -408,7 +408,7 @@ [ "MULTIQC", "multiqc", - "1.33" + "1.35" ] ] } diff --git a/nextflow.config b/nextflow.config index 74ecc89b..af23ed99 100644 --- a/nextflow.config +++ b/nextflow.config @@ -82,7 +82,6 @@ params { email_on_fail = null plaintext_email = false monochrome_logs = false - hook_url = System.getenv('HOOK_URL') help = false help_full = false show_hidden = false @@ -103,6 +102,10 @@ params { validate_params = true } +// Backwards compatibility for publishDir syntax +outputDir = params.outdir +workflow.output.mode = params.publish_dir_mode + // Load base.config by default for all pipelines includeConfig 'conf/base.config' @@ -350,7 +353,7 @@ manifest { description = """Phasing and imputation pipeline""" mainScript = 'main.nf' defaultBranch = 'main' - nextflowVersion = '!>=25.10.0' + nextflowVersion = '!>=25.10.4' version = '1.2.0dev' doi = 'https://doi.org/10.5281/zenodo.14329225' } diff --git a/nextflow_schema.json b/nextflow_schema.json index e473636f..eab2f5d5 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -388,13 +388,6 @@ "fa_icon": "fas fa-palette", "hidden": true }, - "hook_url": { - "type": "string", - "description": "Incoming hook URL for messaging service", - "fa_icon": "fas fa-people-group", - "help_text": "Incoming hook URL for messaging service. Currently, MS Teams and Slack are supported.", - "hidden": true - }, "multiqc_config": { "type": "string", "format": "file-path", diff --git a/nf-test.config b/nf-test.config index 6ecff928..364a91c7 100644 --- a/nf-test.config +++ b/nf-test.config @@ -1,15 +1,18 @@ config { // location for all nf-test tests - testsDir "." + testsDir = "." // nf-test directory including temporary files for each test - workDir System.getenv("NFT_WORKDIR") ?: ".nf-test" + workDir = System.getenv("NFT_WORKDIR") ?: ".nf-test" // location of an optional nextflow.config file specific for executing tests - configFile "tests/nextflow.config" + configFile = "tests/nextflow.config" // ignore tests coming from the nf-core/modules repo - ignore 'modules/nf-core/**/tests/*', 'subworkflows/nf-core/**/tests/*' + ignore = [ + 'modules/nf-core/**/tests/*', + 'subworkflows/nf-core/**/tests/*', + ] // Copy the nextflow_schema.json file to the test directory stage { @@ -17,7 +20,18 @@ config { } // list of filenames or patterns that should be trigger a full test run - triggers 'nextflow.config', 'nf-test.config', 'conf/test.config', 'tests/nextflow.config', 'tests/.nftignore' + triggers = [ + '.github/actions/nf-test/action.yml', + '.github/workflows/nf-test.yml', + 'assets/schema_input.json', + 'bin/*', + 'conf/test.config', + 'nextflow.config', + 'nextflow_schema.json', + 'nf-test.config', + 'tests/.nftignore', + 'tests/nextflow.config', + ] // load the necessary plugins plugins { diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json index 6f0736c1..dd5c8ded 100644 --- a/ro-crate-metadata.json +++ b/ro-crate-metadata.json @@ -1,6 +1,6 @@ { "@context": [ - "https://w3id.org/ro/crate/1.1/context", + "https://w3id.org/ro/crate/1.2/context", { "GithubService": "https://w3id.org/ro/terms/test#GithubService", "JenkinsService": "https://w3id.org/ro/terms/test#JenkinsService", @@ -22,8 +22,8 @@ "@id": "./", "@type": "Dataset", "creativeWorkStatus": "InProgress", - "datePublished": "2026-03-10T15:07:22+00:00", - "description": "

\n \n \n \"nf-core/phaseimpute\"\n \n

\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/nf-core/phaseimpute)\n[![GitHub Actions CI Status](https://github.com/nf-core/phaseimpute/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/phaseimpute/actions/workflows/nf-test.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/phaseimpute/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/phaseimpute/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/phaseimpute/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.14329225-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.14329225)\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%A525.04.0-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-3.5.1-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.5.1)\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/nf-core/phaseimpute)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23phaseimpute-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/phaseimpute)[![Follow on Bluesky](https://img.shields.io/badge/bluesky-%40nf__core-1185fe?labelColor=000000&logo=bluesky)](https://bsky.app/profile/nf-co.re)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)\n\n## Introduction\n\n**nf-core/phaseimpute** is a bioinformatics pipeline to phase and impute genetic data.\n\n\n \n \"metromap\"/\n\n\nThe whole pipeline consists of five main steps, each of which can be run separately and independently. Users are not required to run all steps sequentially and can select specific steps based on their needs:\n\n1. **QC: Chromosome Name Check**: Ensures compatibility by validating that all expected contigs are present in the variant and alignment files.\n\n2. **Simulation (`--simulate`)**: Generates artificial datasets by downsampling high-density data to simulate low-pass genetic information. This enables the comparison of imputation results against a high-quality dataset (truth set). Simulations may include:\n - **Low-pass data generation** by downsampling BAM or CRAM files with [`samtools view -s`](https://www.htslib.org/doc/samtools-view.html) at different depths.\n\n3. **Panel Preparation (`--panelprep`)**: Prepares the reference panel through phasing, quality control, variant filtering, and annotation. Key processes include:\n - **Normalization** of the reference panel to retain essential variants.\n - **Phasing** of haplotypes in the reference panel using [Shapeit5](https://odelaneau.github.io/shapeit5/).\n - **Chunking** of the reference panel into specific regions across chromosomes.\n - **Position Extraction** for targeted imputation sites.\n\n4. **Imputation (`--impute`)**: This is the primary step, where genotypes in the target dataset are imputed using the prepared reference panel. The main steps are:\n - **Imputation** of the target dataset using tools like [Glimpse1](https://odelaneau.github.io/GLIMPSE/glimpse1/index.html), [Glimpse2](https://odelaneau.github.io/GLIMPSE/), [Stitch](https://github.com/rwdavies/stitch), [Quilt](https://github.com/rwdavies/QUILT), [Beagle5](https://faculty.washington.edu/browning/beagle/beagle.html) or [Minimac4](https://github.com/statgen/Minimac4).\n - **Ligation** of imputed chunks to produce a final VCF file per sample, with all chromosomes unified.\n\n5. **Validation (`--validate`)**: Assesses imputation accuracy by comparing the imputed dataset to a truth dataset. This step leverages the [Glimpse2](https://odelaneau.github.io/GLIMPSE/) concordance process to summarize differences between two VCF files.\n\nFor more detailed instructions, please refer to the [usage documentation](https://nf-co.re/phaseimpute/usage).\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\nThe primary function of this pipeline is to impute a target dataset based on a phased panel. Begin by preparing a samplesheet with your input data, formatted as follows:\n\n```csv title=\"samplesheet.csv\"\nsample,file,index\nSAMPLE_1X,/path/to/.,/path/to/.\n```\n\nEach row represents either a bam or a cram file along with its corresponding index file. Ensure that all input files have consistent file extensions.\n\nFor certain tools and steps within the pipeline, you will also need to provide a samplesheet for the reference panel. Here's an example of what a final samplesheet for a reference panel might look like, covering three chromosomes:\n\n```csv title=\"panel.csv\"\npanel,chr,vcf,index\nPhase3,1,ALL.chr1.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz,ALL.chr1.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz.csi\nPhase3,2,ALL.chr2.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz,ALL.chr2.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz.csi\nPhase3,3,ALL.chr3.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz,ALL.chr3.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz.csi\n```\n\n## Running the pipeline\n\nRun one of the steps of the pipeline (imputation with glimpse1) using the following command and test profile:\n\n```bash\nnextflow run nf-core/phaseimpute \\\n -profile test, \\\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/usage/getting_started/configuration#custom-configuration-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/phaseimpute/usage) and the [parameter documentation](https://nf-co.re/phaseimpute/parameters).\n\n## Pipeline output\n\nTo see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/phaseimpute/results) tab on the nf-core website pipeline page.\nFor more details on the output files and reports, please refer to the [output documentation](https://nf-co.re/phaseimpute/output).\n\n## Credits\n\nnf-core/phaseimpute was originally written by Louis Le N\u00e9zet & Anabella Trigila.\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n- Saul Pierotti\n- Eugenia Fontecha\n- Matias Romero Victorica\n- Hemanoel Passarelli\n- Gaspard Ichas\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md). Further development tips can be found in the [development documentation](docs/development.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#phaseimpute` channel](https://nfcore.slack.com/channels/phaseimpute) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\nIf you use nf-core/phaseimpute for your analysis, please cite it using the following doi: [10.5281/zenodo.14329225](https://doi.org/10.5281/zenodo.14329225)\n\nAn extensive list of references for the tools used by the pipeline, including QUILT, GLIMPSE, and STITCH, can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n", + "datePublished": "2026-04-30T13:33:11+00:00", + "description": "

\n \n \n \"nf-core/phaseimpute\"\n \n

\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/nf-core/phaseimpute)\n[![GitHub Actions CI Status](https://github.com/nf-core/phaseimpute/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/phaseimpute/actions/workflows/nf-test.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/phaseimpute/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/phaseimpute/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/phaseimpute/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.14329225-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.14329225)\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-4.0.2-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/4.0.2)\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/nf-core/phaseimpute)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23phaseimpute-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/phaseimpute)[![Follow on Bluesky](https://img.shields.io/badge/bluesky-%40nf__core-1185fe?labelColor=000000&logo=bluesky)](https://bsky.app/profile/nf-co.re)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)\n\n## Introduction\n\n**nf-core/phaseimpute** is a bioinformatics pipeline to phase and impute genetic data.\n\n\n \n \"metromap\"/\n\n\nThe whole pipeline consists of five main steps, each of which can be run separately and independently. Users are not required to run all steps sequentially and can select specific steps based on their needs:\n\n1. **QC: Chromosome Name Check**: Ensures compatibility by validating that all expected contigs are present in the variant and alignment files.\n\n2. **Simulation (`--simulate`)**: Generates artificial datasets by downsampling high-density data to simulate low-pass genetic information. This enables the comparison of imputation results against a high-quality dataset (truth set). Simulations may include:\n - **Low-pass data generation** by downsampling BAM or CRAM files with [`samtools view -s`](https://www.htslib.org/doc/samtools-view.html) at different depths.\n\n3. **Panel Preparation (`--panelprep`)**: Prepares the reference panel through phasing, quality control, variant filtering, and annotation. Key processes include:\n - **Normalization** of the reference panel to retain essential variants.\n - **Phasing** of haplotypes in the reference panel using [Shapeit5](https://odelaneau.github.io/shapeit5/).\n - **Chunking** of the reference panel into specific regions across chromosomes.\n - **Position Extraction** for targeted imputation sites.\n\n4. **Imputation (`--impute`)**: This is the primary step, where genotypes in the target dataset are imputed using the prepared reference panel. The main steps are:\n - **Imputation** of the target dataset using tools like [Glimpse1](https://odelaneau.github.io/GLIMPSE/glimpse1/index.html), [Glimpse2](https://odelaneau.github.io/GLIMPSE/), [Stitch](https://github.com/rwdavies/stitch), [Quilt/Quilt2](https://github.com/rwdavies/QUILT), [Beagle5](https://faculty.washington.edu/browning/beagle/beagle.html) or [Minimac4](https://github.com/statgen/Minimac4).\n - **Ligation** of imputed chunks to produce a final VCF file per sample, with all chromosomes unified.\n\n5. **Validation (`--validate`)**: Assesses imputation accuracy by comparing the imputed dataset to a truth dataset. This step leverages the [Glimpse2](https://odelaneau.github.io/GLIMPSE/) concordance process to summarize differences between two VCF files.\n\nFor more detailed instructions, please refer to the [usage documentation](https://nf-co.re/phaseimpute/usage).\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\nThe primary function of this pipeline is to impute a target dataset based on a phased panel. Begin by preparing a samplesheet with your input data, formatted as follows:\n\n```csv title=\"samplesheet.csv\"\nsample,file,index\nSAMPLE_1X,/path/to/.,/path/to/.\n```\n\nEach row represents either a bam or a cram file along with its corresponding index file. Ensure that all input files have consistent file extensions.\n\nFor certain tools and steps within the pipeline, you will also need to provide a samplesheet for the reference panel. Here's an example of what a final samplesheet for a reference panel might look like, covering three chromosomes:\n\n```csv title=\"panel.csv\"\npanel,chr,vcf,index\nPhase3,1,ALL.chr1.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz,ALL.chr1.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz.csi\nPhase3,2,ALL.chr2.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz,ALL.chr2.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz.csi\nPhase3,3,ALL.chr3.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz,ALL.chr3.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz.csi\n```\n\n## Running the pipeline\n\nRun one of the steps of the pipeline (imputation with glimpse1) using the following command and test profile:\n\n```bash\nnextflow run nf-core/phaseimpute \\\n -profile test, \\\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\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/phaseimpute/usage) and the [parameter documentation](https://nf-co.re/phaseimpute/parameters).\n\n## Pipeline output\n\nTo see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/phaseimpute/results) tab on the nf-core website pipeline page.\nFor more details on the output files and reports, please refer to the [output documentation](https://nf-co.re/phaseimpute/output).\n\n## Credits\n\nnf-core/phaseimpute was originally written by Louis Le N\u00e9zet & Anabella Trigila.\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n- Saul Pierotti\n- Eugenia Fontecha\n- Matias Romero Victorica\n- Hemanoel Passarelli\n- Gaspard Ichas\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](docs/CONTRIBUTING.md). Further development tips can be found in the [development documentation](docs/development.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#phaseimpute` channel](https://nfcore.slack.com/channels/phaseimpute) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\nIf you use nf-core/phaseimpute for your analysis, please cite it using the following doi: [10.5281/zenodo.14329225](https://doi.org/10.5281/zenodo.14329225)\n\nAn extensive list of references for the tools used by the pipeline, including QUILT, GLIMPSE, and STITCH, can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n", "hasPart": [ { "@id": "main.nf" @@ -102,7 +102,7 @@ }, "mentions": [ { - "@id": "#6b9b8e0a-2e44-4e58-a934-5726c0a3604e" + "@id": "#4523c1cb-b6ae-4871-9a4c-c970c6c684a6" } ], "name": "nf-core/phaseimpute" @@ -115,7 +115,7 @@ }, "conformsTo": [ { - "@id": "https://w3id.org/ro/crate/1.1" + "@id": "https://w3id.org/ro/crate/1.2" }, { "@id": "https://w3id.org/workflowhub/workflow-ro-crate/1.0" @@ -129,8 +129,16 @@ "SoftwareSourceCode", "ComputationalWorkflow" ], + "contributor": [ + { + "@id": "#32c13a3a-bd4f-4eed-9cb9-3cf957c074fe" + }, + { + "@id": "#5ec5ec66-4931-45a0-9654-094fab4fb10a" + } + ], "dateCreated": "", - "dateModified": "2026-03-10T16:07:22Z", + "dateModified": "2026-04-30T13:33:11Z", "dct:conformsTo": "https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE/", "keywords": [ "nf-core", @@ -171,14 +179,14 @@ "url": { "@id": "https://www.nextflow.io/" }, - "version": "!>=25.10.0" + "version": "!>=25.10.4" }, { - "@id": "#6b9b8e0a-2e44-4e58-a934-5726c0a3604e", + "@id": "#4523c1cb-b6ae-4871-9a4c-c970c6c684a6", "@type": "TestSuite", "instance": [ { - "@id": "#6267c83d-eae8-4324-b6cf-9861f5620614" + "@id": "#1818bbea-c49a-4561-95c2-e596c87e16cb" } ], "mainEntity": { @@ -187,7 +195,7 @@ "name": "Test suite for nf-core/phaseimpute" }, { - "@id": "#6267c83d-eae8-4324-b6cf-9861f5620614", + "@id": "#1818bbea-c49a-4561-95c2-e596c87e16cb", "@type": "TestInstance", "name": "GitHub Actions workflow for testing nf-core/phaseimpute", "resource": "repos/nf-core/phaseimpute/actions/workflows/nf-test.yml", @@ -319,6 +327,16 @@ "@type": "Organization", "name": "nf-core", "url": "https://nf-co.re/" + }, + { + "@id": "#32c13a3a-bd4f-4eed-9cb9-3cf957c074fe", + "@type": "Person", + "name": "Louis Le Nezet" + }, + { + "@id": "#5ec5ec66-4931-45a0-9654-094fab4fb10a", + "@type": "Person", + "name": "Anabella Trigila" } ] } \ No newline at end of file diff --git a/subworkflows/local/utils_nfcore_phaseimpute_pipeline/main.nf b/subworkflows/local/utils_nfcore_phaseimpute_pipeline/main.nf index 2427d275..ce8fc58c 100644 --- a/subworkflows/local/utils_nfcore_phaseimpute_pipeline/main.nf +++ b/subworkflows/local/utils_nfcore_phaseimpute_pipeline/main.nf @@ -28,7 +28,7 @@ workflow PIPELINE_INITIALISATION { take: version // boolean: Display version and exit validate_params // boolean: Boolean whether to validate parameters against the schema at runtime - _monochrome_logs // boolean: Do not use coloured log outputs + monochrome_logs // boolean: Do not use coloured log outputs nextflow_cli_args // array: List of positional nextflow CLI args outdir // string: The output directory where the results will be saved help // boolean: Display help message and exit @@ -59,7 +59,9 @@ workflow PIPELINE_INITIALISATION { // // Validate parameters and generate parameter summary to stdout // - before_text = """ + + def after_text = "" + def before_text = """ -\033[2m----------------------------------------------------\033[0m- \033[0;32m,--.\033[0;30m/\033[0;32m,-.\033[0m \033[0;34m ___ __ __ __ ___ \033[0;32m/,-._.--~\'\033[0m @@ -76,6 +78,10 @@ workflow PIPELINE_INITIALISATION { * Software dependencies https://github.com/nf-core/phaseimpute/blob/main/CITATIONS.md """ + if (monochrome_logs) { + before_text = before_text.replaceAll(/\033\[[0-9;]*m/, '') + } + command = "nextflow run ${workflow.manifest.name} -profile --input samplesheet.csv --outdir " UTILS_NFSCHEMA_PLUGIN ( @@ -445,7 +451,6 @@ workflow PIPELINE_COMPLETION { outdir // path: Path to output directory where results will be published monochrome_logs // boolean: Disable ANSI colour codes in log output - hook_url // string: hook URL for notifications multiqc_report // string: Path to MultiQC report main: @@ -469,13 +474,11 @@ workflow PIPELINE_COMPLETION { } completionSummary(monochrome_logs) - if (hook_url) { - log.warn("`--hook_url` is set, but the updated nf-core utility subworkflow no longer provides instant messaging notifications. The value will be ignored.") - } + } workflow.onError { - log.error "Pipeline failed. Please refer to troubleshooting docs: https://nf-co.re/docs/usage/troubleshooting" + log.error "Pipeline failed. Please refer to troubleshooting docs for common issues: https://nf-co.re/docs/running/troubleshooting" } } diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf index bf568a08..afca5439 100644 --- a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf +++ b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf @@ -17,7 +17,7 @@ workflow UTILS_NFCORE_PIPELINE { checkProfileProvided(nextflow_cli_args) emit: - valid_config + valid_config = valid_config } /*