Merge branch 'dev' into seqera_containers_example_mod

MatthiasZepper · web-flow · commit 3d953fe0e901 · 2024-10-24T19:19:22.000+02:00
diff --git a/.github/.coveragerc b/.github/.coveragerc
@@ -2,4 +2,3 @@
 omit = nf_core/*-template/*
 source = nf_core
 relative_files = True
-
diff --git a/.github/workflows/changelog.yml b/.github/workflows/changelog.yml
@@ -19,7 +19,7 @@ jobs:
       )
 
     steps:
-      - uses: actions/checkout@eef61447b9ff4aafe5dcd4e0bbf5d482be7e7871 # v4
+      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
         with:
           token: ${{ secrets.NF_CORE_BOT_AUTH_TOKEN }}
 
@@ -36,7 +36,7 @@ jobs:
           fi
           gh pr checkout $PR_NUMBER
 
-      - uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # v5
+      - uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
         with:
           python-version: "3.12"
 
@@ -65,7 +65,7 @@ jobs:
           echo "File changed: ${{ env.changed }}"
 
       - name: Set up Python 3.12
-        uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # v5
+        uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
         with:
           python-version: "3.12"
           cache: "pip"
diff --git a/.github/workflows/create-lint-wf.yml b/.github/workflows/create-lint-wf.yml
@@ -48,12 +48,12 @@ jobs:
           export NXF_WORK=$(pwd)
 
       # Get the repo code
-      - uses: actions/checkout@eef61447b9ff4aafe5dcd4e0bbf5d482be7e7871 # v4
+      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
         name: Check out source-code repository
 
       # Set up nf-core/tools
       - name: Set up Python 3.12
-        uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # v5
+        uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
         with:
           python-version: "3.12"
           cache: pip
diff --git a/.github/workflows/create-test-lint-wf-template.yml b/.github/workflows/create-test-lint-wf-template.yml
@@ -40,7 +40,7 @@ jobs:
       - name: 🏗 Set up yq
         uses: frenck/action-setup-yq@v1
       - name: checkout
-        uses: actions/checkout@eef61447b9ff4aafe5dcd4e0bbf5d482be7e7871 # v4
+        uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
       - name: Create Matrix
         id: create_matrix
         run: |
@@ -77,11 +77,11 @@ jobs:
           cd create-lint-wf-template
           export NXF_WORK=$(pwd)
 
-      - uses: actions/checkout@eef61447b9ff4aafe5dcd4e0bbf5d482be7e7871 # v4
+      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
         name: Check out source-code repository
 
       - name: Set up Python 3.12
-        uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # v5
+        uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
         with:
           python-version: "3.12"
 
diff --git a/.github/workflows/create-test-wf.yml b/.github/workflows/create-test-wf.yml
@@ -48,11 +48,11 @@ jobs:
           cd create-test-wf
           export NXF_WORK=$(pwd)
 
-      - uses: actions/checkout@eef61447b9ff4aafe5dcd4e0bbf5d482be7e7871 # v4
+      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
         name: Check out source-code repository
 
       - name: Set up Python 3.12
-        uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # v5
+        uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
         with:
           python-version: "3.12"
 
diff --git a/.github/workflows/deploy-pypi.yml b/.github/workflows/deploy-pypi.yml
@@ -13,11 +13,11 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/checkout@eef61447b9ff4aafe5dcd4e0bbf5d482be7e7871 # v4
+      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
         name: Check out source-code repository
 
       - name: Set up Python 3.12
-        uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # v5
+        uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
         with:
           python-version: "3.12"
 
diff --git 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@eef61447b9ff4aafe5dcd4e0bbf5d482be7e7871 # v4
+      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
         with:
           token: ${{ secrets.nf_core_bot_auth_token }}
 
@@ -32,7 +32,7 @@ jobs:
           GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }}
 
       # Install and run pre-commit
-      - uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # v5
+      - uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
         with:
           python-version: "3.12"
 
diff --git a/.github/workflows/lint-code.yml b/.github/workflows/lint-code.yml
@@ -18,10 +18,10 @@ jobs:
     env:
       GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
     steps:
-      - uses: actions/checkout@eef61447b9ff4aafe5dcd4e0bbf5d482be7e7871 # v4
+      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
 
       - name: Set up Python 3.12
-        uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # v5
+        uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
         with:
           python-version: "3.12"
           cache: "pip"
diff --git a/.github/workflows/push_dockerhub_dev.yml b/.github/workflows/push_dockerhub_dev.yml
@@ -23,7 +23,7 @@ jobs:
       fail-fast: false
     steps:
       - name: Check out code
-        uses: actions/checkout@eef61447b9ff4aafe5dcd4e0bbf5d482be7e7871 # v4
+        uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
 
       - name: Build nfcore/tools:dev docker image
         run: docker build --no-cache . -t nfcore/tools:dev
diff --git a/.github/workflows/push_dockerhub_release.yml b/.github/workflows/push_dockerhub_release.yml
@@ -23,7 +23,7 @@ jobs:
       fail-fast: false
     steps:
       - name: Check out code
-        uses: actions/checkout@eef61447b9ff4aafe5dcd4e0bbf5d482be7e7871 # v4
+        uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
 
       - name: Build nfcore/tools:latest docker image
         run: docker build --no-cache . -t nfcore/tools:latest
diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
@@ -61,7 +61,7 @@ jobs:
     name: Get test file matrix
     runs-on: "ubuntu-latest"
     steps:
-      - uses: actions/checkout@eef61447b9ff4aafe5dcd4e0bbf5d482be7e7871 # v4
+      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
         name: Check out source-code repository
 
       - name: List tests
@@ -87,11 +87,11 @@ jobs:
           cd pytest
           export NXF_WORK=$(pwd)
 
-      - uses: actions/checkout@eef61447b9ff4aafe5dcd4e0bbf5d482be7e7871 # v4
+      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
         name: Check out source-code repository
 
       - name: Set up Python ${{ needs.setup.outputs.python-version }}
-        uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # v5
+        uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
         with:
           python-version: ${{ needs.setup.outputs.python-version }}
           cache: "pip"
@@ -151,12 +151,14 @@ jobs:
         uses: actions/upload-artifact@b4b15b8c7c6ac21ea08fcf65892d2ee8f75cf882 # v4
         if: always()
         with:
+          include-hidden-files: true
           name: Snapshot Report ${{ env.test }}
           path: ./snapshot_report.html
 
       - name: Upload coverage
         uses: actions/upload-artifact@b4b15b8c7c6ac21ea08fcf65892d2ee8f75cf882 # v4
         with:
+          include-hidden-files: true
           name: coverage_${{ env.test }}
           path: .coverage
 
@@ -170,9 +172,9 @@ jobs:
           mkdir -p pytest
           cd pytest
 
-      - uses: actions/checkout@eef61447b9ff4aafe5dcd4e0bbf5d482be7e7871 # v4
+      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
       - name: Set up Python 3.12
-        uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # v5
+        uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
         env:
           AGENT_TOOLSDIRECTORY: /opt/actions-runner/_work/tools/tools/
         with:
diff --git a/.github/workflows/sync.yml b/.github/workflows/sync.yml
@@ -60,10 +60,10 @@ jobs:
       matrix: ${{fromJson(needs.get-pipelines.outputs.matrix)}}
       fail-fast: false
     steps:
-      - uses: actions/checkout@eef61447b9ff4aafe5dcd4e0bbf5d482be7e7871 # v4
+      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
         name: Check out nf-core/tools
 
-      - uses: actions/checkout@eef61447b9ff4aafe5dcd4e0bbf5d482be7e7871 # v4
+      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
         name: Check out nf-core/${{ matrix.pipeline }}
         with:
           repository: nf-core/${{ matrix.pipeline }}
@@ -73,7 +73,7 @@ jobs:
           fetch-depth: "0"
 
       - name: Set up Python 3.12
-        uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # v5
+        uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
         with:
           python-version: "3.12"
 
diff --git a/.github/workflows/update-textual-snapshots.yml b/.github/workflows/update-textual-snapshots.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@eef61447b9ff4aafe5dcd4e0bbf5d482be7e7871 # v4
+      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
         with:
           token: ${{ secrets.nf_core_bot_auth_token }}
 
@@ -33,7 +33,7 @@ jobs:
 
       # Install dependencies and run pytest
       - name: Set up Python
-        uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # v5
+        uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
         with:
           python-version: "3.12"
           cache: "pip"
diff --git a/.github/workflows/update_components_template.yml b/.github/workflows/update_components_template.yml
@@ -11,10 +11,10 @@ jobs:
 
     steps:
       - name: Checkout repository
-        uses: actions/checkout@eef61447b9ff4aafe5dcd4e0bbf5d482be7e7871 # v4
+        uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
 
       - name: Set up Python
-        uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # v5
+        uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
         with:
           python-version: "3.x"
 
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -1,6 +1,6 @@
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.7.0
+    rev: v0.7.1
     hooks:
       - id: ruff # linter
         args: [--fix, --exit-non-zero-on-fix] # sort imports and fix
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -29,6 +29,8 @@
 - Update python:3.12-slim Docker digest to 032c526 ([#3232](https://github.com/nf-core/tools/pull/3232))
 - use correct `--profile` options for `nf-core subworkflows test` ([#3233](https://github.com/nf-core/tools/pull/3233))
 - Update GitHub Actions ([#3237](https://github.com/nf-core/tools/pull/3237))
+- add `--dir/-d` option to schema commands ([#3247](https://github.com/nf-core/tools/pull/3247))
+- Update pre-commit hook astral-sh/ruff-pre-commit to v0.7.1 ([#3250](https://github.com/nf-core/tools/pull/3250))
 
 ## [v3.0.2 - Titanium Tapir Patch](https://github.com/nf-core/tools/releases/tag/3.0.2) - [2024-10-11]
 
diff --git a/nf_core/__main__.py b/nf_core/__main__.py
@@ -4,6 +4,7 @@
 import logging
 import os
 import sys
+from pathlib import Path
 
 import rich
 import rich.console
@@ -696,12 +697,24 @@ def pipeline_schema():
 
 # nf-core pipelines schema validate
 @pipeline_schema.command("validate")
+@click.option(
+    "-d",
+    "--dir",
+    "directory",
+    type=click.Path(exists=True),
+    default=".",
+    help=r"Pipeline directory. [dim]\[default: current working directory][/]",
+)
 @click.argument("pipeline", required=True, metavar="<pipeline name>")
 @click.argument("params", type=click.Path(exists=True), required=True, metavar="<JSON params file>")
-def command_pipelines_schema_validate(pipeline, params):
+def command_pipelines_schema_validate(directory, pipeline, params):
     """
     Validate a set of parameters against a pipeline schema.
     """
+    if Path(directory, pipeline).exists():
+        # this is a local pipeline
+        pipeline = Path(directory, pipeline)
+
     pipelines_schema_validate(pipeline, params)
 
 
@@ -740,23 +753,39 @@ def command_pipelines_schema_build(directory, no_prompts, web_only, url):
 
 # nf-core pipelines schema lint
 @pipeline_schema.command("lint")
+@click.option(
+    "-d",
+    "--dir",
+    "directory",
+    type=click.Path(exists=True),
+    default=".",
+    help=r"Pipeline directory. [dim]\[default: current working directory][/]",
+)
 @click.argument(
-    "schema_path",
+    "schema_file",
     type=click.Path(exists=True),
     default="nextflow_schema.json",
     metavar="<pipeline schema>",
 )
-def command_pipelines_schema_lint(schema_path):
+def command_pipelines_schema_lint(directory, schema_file):
     """
     Check that a given pipeline schema is valid.
     """
-    pipelines_schema_lint(schema_path)
+    pipelines_schema_lint(Path(directory, schema_file))
 
 
 # nf-core pipelines schema docs
 @pipeline_schema.command("docs")
+@click.option(
+    "-d",
+    "--dir",
+    "directory",
+    type=click.Path(exists=True),
+    default=".",
+    help=r"Pipeline directory. [dim]\[default: current working directory][/]",
+)
 @click.argument(
-    "schema_path",
+    "schema_file",
     type=click.Path(exists=True),
     default="nextflow_schema.json",
     required=False,
@@ -785,11 +814,11 @@ def command_pipelines_schema_lint(schema_path):
     help="CSV list of columns to include in the parameter tables (parameter,description,type,default,required,hidden)",
     default="parameter,description,type,default,required,hidden",
 )
-def command_pipelines_schema_docs(schema_path, output, format, force, columns):
+def command_pipelines_schema_docs(directory, schema_file, output, format, force, columns):
     """
     Outputs parameter documentation for a pipeline schema.
     """
-    pipelines_schema_docs(schema_path, output, format, force, columns)
+    pipelines_schema_docs(Path(directory, schema_file), output, format, force, columns)
 
 
 # nf-core modules subcommands
diff --git a/nf_core/pipeline-template/.github/workflows/ci.yml b/nf_core/pipeline-template/.github/workflows/ci.yml
@@ -45,7 +45,7 @@ jobs:
             profile: "singularity"
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@eef61447b9ff4aafe5dcd4e0bbf5d482be7e7871 # v4
+        uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
 
       - name: Set up Nextflow
         uses: nf-core/setup-nextflow@v2
diff --git a/nf_core/pipeline-template/.github/workflows/download_pipeline.yml b/nf_core/pipeline-template/.github/workflows/download_pipeline.yml
@@ -35,7 +35,7 @@ jobs:
       - name: Disk space cleanup
         uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
 
-      - uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # v5
+      - uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
         with:
           python-version: "3.12"
           architecture: "x64"
diff --git a/nf_core/pipeline-template/.github/workflows/fix-linting.yml b/nf_core/pipeline-template/.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@eef61447b9ff4aafe5dcd4e0bbf5d482be7e7871 # v4
+      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
         with:
           token: ${{ secrets.nf_core_bot_auth_token }}
 
@@ -32,7 +32,7 @@ jobs:
           GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }}
 
       # Install and run pre-commit
-      - uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # v5
+      - uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
         with:
           python-version: "3.12"
 
diff --git a/nf_core/pipeline-template/.github/workflows/linting.yml b/nf_core/pipeline-template/.github/workflows/linting.yml
diff --git a/nf_core/pipeline-template/.github/workflows/release-announcements.yml b/nf_core/pipeline-template/.github/workflows/release-announcements.yml
diff --git a/nf_core/pipeline-template/.github/workflows/template_version_comment.yml b/nf_core/pipeline-template/.github/workflows/template_version_comment.yml
diff --git a/tests/test_cli.py b/tests/test_cli.py
