Merge branch 'dev' into api_schema_description

.github/ISSUE_TEMPLATE/bug_report.yml

@@ -38,4 +38,4 @@ body:
         * Executor _(eg. slurm, local, awsbatch)_
         * OS _(eg. CentOS Linux, macOS, Linux Mint)_
         * Version of nf-core/tools _(eg. 1.1, 1.5, 1.8.2)_
-        * Python version _(eg. 3.7, 3.8)_
+        * Python version _(eg. 3.10, 3.11)_

.github/RELEASE_CHECKLIST.md

@@ -8,8 +8,8 @@
 6. Create a PR from `dev` to `master`
 7. Make sure all CI tests are passing again (additional tests are run on PRs to `master`)
 8. Request review (2 approvals required)
-9. Merge the PR into `master`
-10. Run `rich-codex` to regenerate docs screengrabs (actions `workflow_dispatch` button)
+9. Run `rich-codex` to regenerate docs screengrabs (actions `workflow_dispatch` button)
+10. Merge the PR into `master`
 11. Wait for CI tests on the commit to passed
 12. (Optional but a good idea) Run a manual sync on `nf-core/testpipeline` and check that CI is passing on the resulting PR.
 13. Create a new release copying the `CHANGELOG` for that release into the description section.

.github/workflows/branch.yml

@@ -13,7 +13,7 @@ jobs:
       - name: Check PRs
         if: github.repository == 'nf-core/tools'
         run: |
-          { [[ ${{github.event.pull_request.head.repo.full_name}} == nf-core/tools ]] && [[ $GITHUB_HEAD_REF = "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]]
+          { [[ ${{github.event.pull_request.head.repo.full_name}} == nf-core/tools ]] && [[ $GITHUB_HEAD_REF == "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]]
 
       # If the above check failed, post a comment on the PR explaining the failure
       - name: Post PR comment

.github/workflows/create-test-wf.yml

@@ -29,10 +29,10 @@ jobs:
       - uses: actions/checkout@v3
         name: Check out source-code repository
 
-      - name: Set up Python 3.7
+      - name: Set up Python 3.8
         uses: actions/setup-python@v4
         with:
-          python-version: 3.7
+          python-version: 3.8
 
       - name: Install python dependencies
         run: |

.github/workflows/deploy-pypi.yml

@@ -16,10 +16,10 @@ jobs:
       - uses: actions/checkout@v3
         name: Check out source-code repository
 
-      - name: Set up Python 3.7
+      - name: Set up Python 3.8
         uses: actions/setup-python@v4
         with:
-          python-version: 3.7
+          python-version: 3.8
 
       - name: Install python dependencies
         run: |

.github/workflows/pytest.yml

@@ -19,7 +19,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.7", "3.8", "3.9", "3.10", "3.11"]
+        python-version: ["3.8", "3.9", "3.10", "3.11"]
 
     steps:
       - uses: actions/checkout@v3

.github/workflows/tools-api-docs-dev.yml

@@ -22,10 +22,10 @@ jobs:
       - name: Check out source-code repository
         uses: actions/checkout@v3
 
-      - name: Set up Python 3.7
+      - name: Set up Python 3.8
         uses: actions/setup-python@v4
         with:
-          python-version: 3.7
+          python-version: 3.8
 
       - name: Install python dependencies
         run: |

.github/workflows/tools-api-docs-release.yml

@@ -21,10 +21,10 @@ jobs:
       - name: Check out source-code repository
         uses: actions/checkout@v3
 
-      - name: Set up Python 3.7
+      - name: Set up Python 3.8
         uses: actions/setup-python@v4
         with:
-          python-version: 3.7
+          python-version: 3.8
 
       - name: Install python dependencies
         run: |

.pre-commit-config.yaml

@@ -1,14 +1,13 @@
 repos:
   - repo: https://github.com/psf/black
-    rev: 22.3.0
+    rev: 23.1.0
     hooks:
       - id: black
-        language_version: python3.9
   - repo: https://github.com/pycqa/isort
-    rev: 5.10.1
+    rev: 5.12.0
     hooks:
       - id: isort
   - repo: https://github.com/pre-commit/mirrors-prettier
-    rev: "v2.6.2"
+    rev: "v2.7.1"
     hooks:
       - id: prettier

.prettierignore

@@ -3,4 +3,5 @@ adaptivecard.json
 slackreport.json
 docs/api/_build
 testing
-
+nf_core/module-template/modules/meta.yml
+nf_core/module-template/tests/test.yml

CHANGELOG.md

@@ -1,11 +1,38 @@
 # nf-core/tools: Changelog
 
+# v2.8dev
+
+### Template
+
+- Turn on automatic clean up of intermediate files in `work/` on successful pipeline completion in full-test config ([#2163](https://github.com/nf-core/tools/pull/2163)) [Contributed by @jfy133]
+- Add documentation to `usage.md` on how to use `params.yml` files, based on nf-core/ampliseq text ([#2173](https://github.com/nf-core/tools/pull/2173/)) [Contributed by @jfy133, @d4straub]
+- Make jobs automatically resubmit for a much wider range of exit codes (now `104` and `130..145`) ([#2170](https://github.com/nf-core/tools/pull/2170))
+- Remove problematic sniffer code in samplesheet_check.py that could give false positive 'missing header' errors ([https://github.com/nf-core/tools/pull/2194]) [Contributed by @Midnighter, @jfy133]
+- Consistent syntax for branch checks in PRs ([#2202](https://github.com/nf-core/tools/issues/2202))
+- Fixed minor Jinja2 templating bug that caused the PR template to miss a newline
+
+### Linting
+
+### Modules
+
+- Add an `--empty-template` option to create a module without TODO statements or examples ([#2175](https://github.com/nf-core/tools/pull/2175) & [#2177](https://github.com/nf-core/tools/pull/2177))
+
+### Subworkflows
+
+- Fixing problem when a module included in a subworkflow had a name change from TOOL to TOOL/SUBTOOL ([#2177](https://github.com/nf-core/tools/pull/2177))
+- Fix `nf-core subworkflows test` not running subworkflow tests ([#2181](https://github.com/nf-core/tools/pull/2181))
+
+### General
+
+- `nf-core modules/subworkflows info` now prints the include statement for the module/subworkflow ([#2182](https://github.com/nf-core/tools/pull/2182)).
+
 ## [v2.7.2 - Mercury Eagle Patch](https://github.com/nf-core/tools/releases/tag/2.7.2) - [2022-12-19]
 
 ### Template
 
 - Fix the syntax of github_output in GitHub actions ([#2114](https://github.com/nf-core/tools/pull/2114))
 - Fix a bug introduced in 2.7 that made pipelines hang ([#2132](https://github.com/nf-core/tools/issues/2132))
+- Explicitly disable `conda` when a container profile ([#2140](https://github.com/nf-core/tools/pull/2140))
 
 ### Linting
 
@@ -17,6 +44,7 @@
 - Only check that a pipeline name doesn't contain dashes if the name is provided by prompt of `--name`. Don't check if a template file is used. ([#2123](https://github.com/nf-core/tools/pull/2123))
 - Deprecate `--enable_conda` parameter. Use `conda.enable` instead ([#2131](https://github.com/nf-core/tools/pull/2131))
 - Handle `json.load()` exceptions ([#2134](https://github.com/nf-core/tools/pull/2134))
+- Deprecate Python 3.7 support because it reaches EOL ([#2210](https://github.com/nf-core/tools/pull/2210))
 
 ## [v2.7.1 - Mercury Eagle Patch](https://github.com/nf-core/tools/releases/tag/2.7.1) - [2022-12-08]
 
@@ -49,7 +77,8 @@ Another big release with lots of new features and bug fixes. Thanks to all contr
 
 - Fix lint warnings for `samplesheet_check.nf` module ([#1875](https://github.com/nf-core/tools/pull/1875)).
 - Check that the workflow name provided with a template doesn't contain dashes ([#1822](https://github.com/nf-core/tools/pull/1822))
-- Remove `CITATION.cff` file from pipeline template, to avoid that pipeline Zenodo entries reference the nf-core publication instead of the pipeline ([#2059](https://github.com/nf-core/tools/pull/2059)).
+- Remove `CITATION.cff` file from pipeline template, to avoid that pipeline Zenodo entries reference the nf-core publication instead of the pipeline ([#2059](https://github.com/nf-core/tools/pull/2059)).- Add initial CHM13 support ([1988](https://github.com/nf-core/tools/issues/1988))
+- Add initial CHM13 support ([1988](https://github.com/nf-core/tools/issues/1988))
 
 ### Linting
 

README.md

@@ -344,6 +344,8 @@ You can run the pipeline by simply providing the directory path for the `workflo
 nextflow run /path/to/download/nf-core-rnaseq-dev/workflow/ --input mydata.csv --outdir results  # usual parameters here
 ```
 
+> Note that if you downloaded singularity images, you will need to use `-profile singularity` or have it enabled in your config file.
+
 ### Downloaded nf-core configs
 
 The pipeline files are automatically updated (`params.custom_config_base` is set to `../configs`), so that the local copy of institutional configs are available when running the pipeline.
@@ -1041,6 +1043,8 @@ To list subworkflows installed in a local pipeline directory you can use `nf-cor
 
 <!-- RICH-CODEX
 working_dir: tmp/nf-core-nextbigthing
+before_command: >
+  echo "repository_type: pipeline" >> .nf-core.yml
 head: 25
 -->
 
@@ -1054,6 +1058,8 @@ This shows documentation about the subworkflow on the command line, similar to w
 
 <!-- RICH-CODEX
 working_dir: tmp/nf-core-nextbigthing
+before_command: >
+  echo "repository_type: pipeline" >> .nf-core.yml
 -->
 
 ![`nf-core subworkflows info bam_rseqc`](docs/images/nf-core-subworkflows-info.svg)
@@ -1065,6 +1071,8 @@ A subworkflow installed this way will be installed to the `./subworkflows/nf-cor
 
 <!-- RICH-CODEX
 working_dir: tmp/nf-core-nextbigthing
+before_command: >
+  echo "repository_type: pipeline" >> .nf-core.yml
 -->
 
 ![`nf-core subworkflows install bam_rseqc`](docs/images/nf-core-subworkflows-install.svg)
@@ -1084,6 +1092,8 @@ You can update subworkflows installed from a remote repository in your pipeline
 
 <!-- RICH-CODEX
 working_dir: tmp/nf-core-nextbigthing
+before_command: >
+  echo "repository_type: pipeline" >> .nf-core.yml
 -->
 
 ![`nf-core subworkflows update --all --no-preview`](docs/images/nf-core-subworkflows-update.svg)
@@ -1143,6 +1153,8 @@ To delete a subworkflow from your pipeline, run `nf-core subworkflows remove`.
 
 <!-- RICH-CODEX
 working_dir: tmp/nf-core-nextbigthing
+before_command: >
+  echo "repository_type: pipeline" >> .nf-core.yml
 -->
 
 ![`nf-core subworkflows remove bam_rseqc`](docs/images/nf-core-subworkflows-remove.svg)
@@ -1171,10 +1183,10 @@ The `nf-core subworkflows create` command will prompt you with the relevant ques
 <!-- RICH-CODEX
 working_dir: tmp
 before_command: git clone https://github.com/nf-core/modules.git && cd modules
-fake_command: nf-core subworkflows create bam_stats_samtools --author @nf-core-bot  --label process_low --meta --force
+fake_command: nf-core subworkflows create bam_stats_samtools --author @nf-core-bot --force
 -->
 
-![`cd modules && nf-core subworkflows create bam_stats_samtools --author @nf-core-bot  --label process_low --meta --force`](docs/images/nf-core-subworkflows-create.svg)
+![`cd modules && nf-core subworkflows create bam_stats_samtools --author @nf-core-bot --force`](docs/images/nf-core-subworkflows-create.svg)
 
 ### Create a subworkflow test config file
 
@@ -1186,6 +1198,8 @@ After you have written a minimal Nextflow script to test your subworkflow in `/t
 working_dir: tmp/subworkflows
 extra_env:
   PROFILE: 'conda'
+before_command: >
+  echo "repository_type: modules" >> .nf-core.yml
 -->
 
 ![`nf-core subworkflows create-test-yml bam_stats_samtools --no-prompts --force`](docs/images/nf-core-subworkflows-create-test.svg)
@@ -1201,6 +1215,8 @@ working_dir: tmp/subworkflows
 timeout: 30
 extra_env:
   PROFILE: 'conda'
+before_command: >
+  echo "repository_type: pipeline" >> .nf-core.yml
 -->
 
 ![`nf-core subworkflows test bam_rseqc --no-prompts`](docs/images/nf-core-subworkflows-test.svg)

nf_core/.pre-commit-prettier-config.yaml

@@ -1,5 +1,5 @@
 repos:
   - repo: https://github.com/pre-commit/mirrors-prettier
-    rev: "v2.6.2"
+    rev: "v2.7.1"
     hooks:
       - id: prettier

nf_core/__main__.py

@@ -678,7 +678,16 @@ def remove(ctx, dir, tool):
 @click.option("-f", "--force", is_flag=True, default=False, help="Overwrite any files if they already exist")
 @click.option("-c", "--conda-name", type=str, default=None, help="Name of the conda package to use")
 @click.option("-p", "--conda-package-version", type=str, default=None, help="Version of conda package to use")
-def create_module(ctx, tool, dir, author, label, meta, no_meta, force, conda_name, conda_package_version):
+@click.option(
+    "-i",
+    "--empty-template",
+    is_flag=True,
+    default=False,
+    help="Create a module from the template without TODOs or examples",
+)
+def create_module(
+    ctx, tool, dir, author, label, meta, no_meta, force, conda_name, conda_package_version, empty_template
+):
     """
     Create a new DSL2 module from the nf-core template.
 
@@ -700,7 +709,7 @@ def create_module(ctx, tool, dir, author, label, meta, no_meta, force, conda_nam
     # Run function
     try:
         module_create = nf_core.modules.ModuleCreate(
-            dir, tool, author, label, has_meta, force, conda_name, conda_package_version
+            dir, tool, author, label, has_meta, force, conda_name, conda_package_version, empty_template
         )
         module_create.create()
     except UserWarning as e:
@@ -1446,8 +1455,7 @@ def docs(schema_path, output, format, force, columns):
     # Assume we're in a pipeline dir root if schema path not set
     schema_obj.get_schema_path(schema_path)
     schema_obj.load_schema()
-    if not output:
-        stdout.print(schema_obj.print_documentation(output, format, force, columns.split(",")))
+    schema_obj.print_documentation(output, format, force, columns.split(","))
 
 
 # nf-core bump-version

nf_core/bump_version.py

@@ -133,12 +133,10 @@ def update_file_version(filename, pipeline_obj, patterns):
 
     replacements = []
     for pattern in patterns:
-
         found_match = False
 
         newcontent = []
         for line in content.splitlines():
-
             # Match the pattern
             matches_pattern = re.findall(rf"^.*{pattern[0]}.*$", line)
             if matches_pattern: