Merge branch 'dev' into set_conda_enabled

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

@@ -21,7 +21,7 @@ jobs:
  - "latest-everything"
  steps:
  # Get the repo code
- - uses: actions/checkout@v2
+ - uses: actions/checkout@v3
  name: Check out source-code repository
 
  # Set up nf-core/tools

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

@@ -20,7 +20,7 @@ jobs:
  - "21.10.3"
  - "latest-everything"
  steps:
- - uses: actions/checkout@v2
+ - uses: actions/checkout@v3
  name: Check out source-code repository
 
  - name: Set up Python 3.7

.github/workflows/deploy-pypi.yml

@@ -13,7 +13,7 @@ jobs:
  runs-on: ubuntu-latest
 
  steps:
- - uses: actions/checkout@v2
+ - uses: actions/checkout@v3
  name: Check out source-code repository
 
  - name: Set up Python 3.7

.github/workflows/lint-code.yml

@@ -10,7 +10,7 @@ jobs:
  EditorConfig:
  runs-on: ubuntu-latest
  steps:
- - uses: actions/checkout@v2
+ - uses: actions/checkout@v3
 
  - uses: actions/setup-node@v2
 
@@ -24,7 +24,7 @@ jobs:
  Prettier:
  runs-on: ubuntu-latest
  steps:
- - uses: actions/checkout@v2
+ - uses: actions/checkout@v3
 
  - uses: actions/setup-node@v2
 
@@ -37,7 +37,7 @@ jobs:
  PythonBlack:
  runs-on: ubuntu-latest
  steps:
- - uses: actions/checkout@v2
+ - uses: actions/checkout@v3
 
  - name: Check code lints with Black
  uses: psf/black@stable
@@ -68,7 +68,7 @@ jobs:
  runs-on: ubuntu-latest
  steps:
  - name: Check out source-code repository
- uses: actions/checkout@v2
+ uses: actions/checkout@v3
 
  - name: Set up Python 3.8
  uses: actions/setup-python@v2

.github/workflows/push_dockerhub_dev.yml

@@ -23,7 +23,7 @@ jobs:
  fail-fast: false
  steps:
  - name: Check out code
- uses: actions/checkout@v2
+ uses: actions/checkout@v3
 
  - name: Build nfcore/tools:dev docker image
  run: docker build --no-cache . -t nfcore/tools:dev

.github/workflows/push_dockerhub_release.yml

@@ -23,7 +23,7 @@ jobs:
  fail-fast: false
  steps:
  - name: Check out code
- uses: actions/checkout@v2
+ uses: actions/checkout@v3
 
  - name: Build nfcore/tools:latest docker image
  run: docker build --no-cache . -t nfcore/tools:latest
@@ -38,5 +38,5 @@ jobs:
  docker tag nfcore/tools:latest nfcore/tools:${{ github.event.release.tag_name }}
  docker push nfcore/tools:${{ github.event.release.tag_name }}
  docker push nfcore/gitpod:latest
- docker tag nfcore/gitpod:latest nfcore/tools:${{ github.event.release.tag_name }}
+ docker tag nfcore/gitpod:latest nfcore/gitpod:${{ github.event.release.tag_name }}
  docker push nfcore/gitpod:${{ github.event.release.tag_name }}

.github/workflows/pytest.yml

@@ -18,7 +18,7 @@ jobs:
  python-version: ["3.7", "3.8", "3.9", "3.10"]
 
  steps:
- - uses: actions/checkout@v2
+ - uses: actions/checkout@v3
  name: Check out source-code repository
 
  - name: Set up Python ${{ matrix.python-version }}

.github/workflows/sync.yml

@@ -36,10 +36,10 @@ jobs:
  matrix: ${{fromJson(needs.get-pipelines.outputs.matrix)}}
  fail-fast: false
  steps:
- - uses: actions/checkout@v2
+ - uses: actions/checkout@v3
  name: Check out nf-core/tools
 
- - uses: actions/checkout@v2
+ - uses: actions/checkout@v3
  name: Check out nf-core/${{ matrix.pipeline }}
  with:
  repository: nf-core/${{ matrix.pipeline }}

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

@@ -14,7 +14,7 @@ jobs:
 
  steps:
  - name: Check out source-code repository
- uses: actions/checkout@v2
+ uses: actions/checkout@v3
 
  - name: Set up Python 3.7
  uses: actions/setup-python@v3

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

@@ -19,7 +19,7 @@ jobs:
  - ${{ github.event.release.tag_name }}
  steps:
  - name: Check out source-code repository
- uses: actions/checkout@v2
+ uses: actions/checkout@v3
 
  - name: Set up Python 3.7
  uses: actions/setup-python@v3

CHANGELOG.md

@@ -1,9 +1,33 @@
 # nf-core/tools: Changelog
 
+## v2.7dev
+
+### Template
+
+- Fix lint warnings for `samplesheet_check.nf` module
+
+### Linting
+
+### General
+
+- Fix error in tagging GitPod docker images during releases
+- `nf-core sync` now supports the template YAML file using `-t/--template-yaml`.
+- Fix bug when updating modules from old version in old folder structure
+- Don't remove local copy of modules repo, only update it with fetch ([#1881](https://github.com/nf-core/tools/pull/1881))
+- Add subworkflow commands create-test-yml, create and install ([#1897](https://github.com/nf-core/tools/pull/1897))
+- Update subworkflows install so it installs also imported modules and subworkflows ([#1904](https://github.com/nf-core/tools/pull/1904))
+- Improve test coverage of sync.py
+- `check_up_to_date()` function from `modules_json` also checks for subworkflows.
+
+### Modules
+
+- Update patch file paths if the modules directory has the old structure ([#1878](https://github.com/nf-core/tools/pull/1878))
+
 ## [v2.6 - Tin Octopus](https://github.com/nf-core/tools/releases/tag/2.6) - [2022-10-04]
 
 ### Template
 
+- Add template for subworkflows
 - Add `actions/upload-artifact` step to the awstest workflows, to expose the debug log file
 - Add `prettier` as a requirement to Gitpod Dockerimage
 - Bioconda incompatible conda channel setups now result in more informative error messages ([#1812](https://github.com/nf-core/tools/pull/1812))
@@ -26,6 +50,7 @@
 - Schema: Remove `allOf` if no definition groups are left.
 - Use contextlib to temporarily change working directories ([#1819](https://github.com/nf-core/tools/pull/1819))
 - More helpful error messages if `nf-core download` can't parse a singularity image download
+- Add `nf-core subworkflows create` command
 
 ### Modules
 
@@ -40,6 +65,10 @@
 - Lint pyproject.toml file exists and content ([#1795](https://github.com/nf-core/tools/pull/1795))
 - Update GitHub PyPI package release action to v1 ([#1785](https://github.com/nf-core/tools/pull/1785))
 
+### Template
+
+- Update GitHub actions to use nodejs16 ([#1944](https://github.com/nf-core/tools/pull/1944))
+
 ## [v2.5 - Gold Otter](https://github.com/nf-core/tools/releases/tag/2.5) - [2022-08-30]
 
 ### Template

MANIFEST.in

@@ -2,4 +2,5 @@ include LICENSE
 include README.md
 graft nf_core/module-template
 graft nf_core/pipeline-template
+graft nf_core/subworkflow-template
 include requirements.txt

README.md

@@ -17,6 +17,7 @@ A python package with helper tools for the nf-core community.
 ## Table of contents <!-- omit in toc -->
 
 - [`nf-core` tools installation](#installation)
+- [`nf-core` tools update](#update-tools)
 - [`nf-core list` - List available pipelines](#listing-pipelines)
 - [`nf-core launch` - Run a pipeline with interactive parameter prompts](#launch-a-pipeline)
 - [`nf-core download` - Download pipeline for offline use](#downloading-pipelines-for-offline-use)
@@ -186,6 +187,22 @@ If you would prefer to skip this check, set the environment variable `NFCORE_NO_
 export NFCORE_NO_VERSION_CHECK=1
 ```
 
+### Update tools
+
+It is advisable to keep nf-core/tools updated to the most recent version. The command to update depends on the system used to install it, for example if you have installed it with conda you can use:
+
+```bash
+conda update nf-core
+```
+
+if you used pip:
+
+```bash
+pip install --upgrade nf-core
+```
+
+Please refer to the respective documentation for further details to manage packages, as for example [conda](https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-pkgs.html#updating-packages) or [pip](https://packaging.python.org/en/latest/tutorials/installing-packages/#upgrading-packages).
+
 ## Listing pipelines
 
 The command `nf-core list` shows all available nf-core pipelines along with their latest version, when that was published and how recently the pipeline code was pulled to your local system (if at all).
@@ -216,7 +233,7 @@ Archived pipelines are not returned by default. To include them, use the `--show
 ## Launch a pipeline
 
 Some nextflow pipelines have a considerable number of command line flags that can be used.
-To help with this, you can use the `nf-core launch` command
+To help with this, you can use the `nf-core launch` command.
 You can choose between a web-based graphical interface or an interactive command-line wizard tool to enter the pipeline parameters for your run.
 Both interfaces show documentation alongside each parameter and validate your inputs.
 
@@ -500,7 +517,7 @@ To help developers working with pipeline schema, nf-core tools has three `schema
 Nextflow can take input parameters in a JSON or YAML file when running a pipeline using the `-params-file` option.
 This command validates such a file against the pipeline schema.
 
-`Usage is `nf-core schema validate <pipeline> <parameter file>`. eg with the pipeline downloaded [above](#download-pipeline), you can run:
+Usage is `nf-core schema validate <pipeline> <parameter file>`. eg with the pipeline downloaded [above](#download-pipeline), you can run:
 
 <!-- RICH-CODEX
 working_dir: tmp