Merge branch 'dev' of https://github.com/nf-core/tools into maxulysse…

…-patch-1

.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

@@ -3,7 +3,7 @@
 1. Check issue milestones to see outstanding issues to resolve if possible or transfer to the milestones for the next release e.g. [`v1.9`](https://github.com/nf-core/tools/issues?q=is%3Aopen+is%3Aissue+milestone%3A1.9)
 2. Most importantly, pick an undeniably outstanding [name](http://www.codenamegenerator.com/) for the release where _Prefix_ = _Metal_ and _Dictionary_ = _Animal_.
 3. Check the [pipeline health page](https://nf-co.re/pipeline_health) to make sure that all repos look sane (missing `TEMPLATE` branches etc)
-4. Create a PR to `dev` to bump the version in `CHANGELOG.md` and `setup.py`.
+4. Create a PR to `dev` to bump the version in `CHANGELOG.md` and `setup.py` and change the gitpod container to `nfcore/gitpod:latest`.
 5. Make sure all CI tests are passing!
 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`)
@@ -19,4 +19,4 @@
 1. Check the automated template synchronisation has been triggered properly. This should automatically open PRs directly to individual pipeline repos with the appropriate changes to update the pipeline template.
 2. Check that the automatic `PyPi` deployment has worked: [pypi.org/project/nf-core](https://pypi.org/project/nf-core/)
 3. Check `BioConda` has an automated PR to bump the version, and merge. eg. [bioconda/bioconda-recipes #20065](https://github.com/bioconda/bioconda-recipes/pull/20065)
-4. Create a tools PR to `dev` to bump back to the next development version in `CHANGELOG.md` and `setup.py`
+4. Create a tools PR to `dev` to bump back to the next development version in `CHANGELOG.md` and `setup.py` and change the gitpod container to `nfcore/gitpod:dev`.

.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-frozen-ubuntu-20.04.yml

@@ -33,6 +33,7 @@ jobs:
 
       - name: Downgrade git to the Ubuntu official repository's version
         run: |
+          sudo apt update
           sudo apt remove git git-man
           sudo add-apt-repository --remove ppa:git-core/ppa
           sudo apt install git

.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/stale.yml

@@ -0,0 +1,24 @@
+name: "Close stale issues and stale PRs"
+on:
+  schedule:
+    - cron: "30 1 * * 7" # Once a week
+
+jobs:
+  stale:
+    runs-on: ubuntu-latest
+    permissions:
+      issues: write
+      pull-requests: write
+    steps:
+      - uses: actions/stale@v7
+        with:
+          stale-issue-message: "This issue is stale because it has been inactive for more than 30 days. More information is required. Remove stale label or comment or this will be closed in 20 days."
+          stale-pr-message: "This PR is stale because it has been open more than 45 days with no activity. Remove stale label or comment if it is still useful. In any case a PR will be automatically closed."
+          close-issue-message: "This issue was closed because it has been stalled for 20 days with no activity."
+          days-before-stale: 30
+          days-before-close: 20
+          days-before-pr-close: -1
+          any-of-labels: "awaiting-changes,awaiting-feedback"
+          exempt-issue-labels: "WIP"
+          exempt-pr-labels: "WIP"
+          repo-token: ${{ secrets.GITHUB_TOKEN }}

.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: |

.gitpod.yml

@@ -1,4 +1,4 @@
-image: nfcore/gitpod:latest
+image: nfcore/gitpod:dev
 tasks:
   - name: install current state of nf-core/tools and setup pre-commit
     command: |

.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

@@ -4,14 +4,40 @@
 
 ### 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))
+- Add a stale GHA wich stale + close issues and stale PRs with specific labels ([#2183](https://github.com/nf-core/tools/pull/2183))
+- 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
+- Updated AWS tests to use newly moved `seqeralabs/action-tower-launch` instead of `nf-core/tower-action`
+
 ### Linting
 
+- Update modules lint test to fail if enable_conda is found ([#2213](https://github.com/nf-core/tools/pull/2213))
+- Read module lint configuration from `.nf-core.yml`, not `.nf-core-lint.yml` ([#2221](https://github.com/nf-core/tools/pull/2221))
+- `nf-core schema lint` now defaults to linting `nextflow_schema.json` if no filename is provided ([#2225](https://github.com/nf-core/tools/pull/2225))
+
 ### 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))
+- Add tests for `nf-core subworkflows create-test-yml` ([#2219](https://github.com/nf-core/tools/pull/2219))
+
 ### General
 
+- `nf-core modules/subworkflows info` now prints the include statement for the module/subworkflow ([#2182](https://github.com/nf-core/tools/pull/2182)).
+- Add a stale GHA wich stale + close issues and stale PRs with specific labels ([#2183](https://github.com/nf-core/tools/pull/2183))
+- update minimum version of rich to 13.3.1 ([#2185](https://github.com/nf-core/tools/pull/2185))
+- Add the Nextflow version to Gitpod container matching the minimal Nextflow version for nf-core (according to `nextflow.config`) ([#2196](https://github.com/nf-core/tools/pull/2196))
+- Use `nfcore/gitpod:dev` container in the dev branch ([#2196](https://github.com/nf-core/tools/pull/2196))
+- Replace requests_mock with responses in test mocks ([#2165](https://github.com/nf-core/tools/pull/2165)).
+
 ## [v2.7.2 - Mercury Eagle Patch](https://github.com/nf-core/tools/releases/tag/2.7.2) - [2022-12-19]
 
 ### Template
@@ -30,6 +56,7 @@
 - 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]
 
@@ -62,7 +89,8 @@ 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.
@@ -608,26 +610,37 @@ If you want to add a parameter to the schema, you first have to add the paramete
 
 The graphical interface is oganzised in groups and within the groups the single parameters are stored. For a better overview you can collapse all groups with the `Collapse groups` button, then your new parameters will be the only remaining one at the bottom of the page. Now you can either create a new group with the `Add group` button or drag and drop the paramters in an existing group. Therefor the group has to be expanded. The group title will be displayed, if you run your pipeline with the `--help` flag and its description apears on the parameter page of your pipeline.
 
-Now you can start to change the parameter itself. The description is a short explanation about the parameter, that apears if you run your pipeline with the `--help` flag. By clicking on the dictionary icon you can add a longer explanation for the parameter page of your pipeline. If you want to specify some conditions for your parameter, like the file extension, you can use the nut icon to open the settings. This menu depends on the `type` you assigned to your parameter. For intergers you can define a min and max value, and for strings the file extension can be specified.
+Now you can start to change the parameter itself. The `ID` of a new parameter should be defined in small letters without whitespaces. The description is a short free text explanation about the parameter, that appears if you run your pipeline with the `--help` flag. By clicking on the dictionary icon you can add a longer explanation for the parameter page of your pipeline. Usually, they contain a small paragraph about the parameter settings or a used datasource, like databases or references. If you want to specify some conditions for your parameter, like the file extension, you can use the nut icon to open the settings. This menu depends on the `type` you assigned to your parameter. For integers you can define a min and max value, and for strings the file extension can be specified.
+
+The `type` field is one of the most important points in your pipeline schema, since it defines the datatype of your input and how it will be interpreted. This allows extensive testing prior to starting the pipeline.
+
+The basic datatypes for a pipeline schema are:
 
-After you filled your schema, click on the `Finished` button in the top rigth corner, this will automatically update your `nextflow_schema.json`. If this is not working you can copy the schema from the graphical interface and paste it in your `nextflow_schema.json` file.
+- `string`
+- `number`
+- `integer`
+- `boolean`
+
+For the `string` type you have three different options in the settings (nut icon): `enumerated values`, `pattern` and `format`. The first option, `enumerated values`, allows you to specify a list of specific input values. The list has to be separated with a pipe. The `pattern` and `format` settings can depend on each other. The `format` has to be either a directory or a file path. Depending on the `format` setting selected, specifying the `pattern` setting can be the most efficient and time saving option, especially for `file paths`. The `number` and `integer` types share the same settings. Similarly to `string`, there is an `enumerated values` option with the possibility of specifying a `min` and `max` value. For the `boolean` there is no further settings and the default value is usually `false`. The `boolean` value can be switched to `true` by adding the flag to the command. This parameter type is often used to skip specific sections of a pipeline.
+
+After filling the schema, click on the `Finished` button in the top right corner, this will automatically update your `nextflow_schema.json`. If this is not working, the schema can be copied from the graphical interface and pasted in your `nextflow_schema.json` file.
 
 ### Update existing pipeline schema
 
-Important for the update of a pipeline schema is, that if you want to change the default value of a parameter, you should change it in the `nextflow.config` file, since the value in the config file overwrites the value in the pipeline schema. To change any other parameter use `nf-core schema build --web-only` to open the graphical interface without rebuilding the pipeline schema. Now, you can change your parameters as mentioned above but keep in mind that changing the parameter datatype is depending on the default value you specified in the `nextflow.config` file.
+It's important to change the default value of a parameter in the `nextflow.config` file first and then in the pipeline schema, because the value in the config file overwrites the value in the pipeline schema. To change any other parameter use `nf-core schema build --web-only` to open the graphical interface without rebuilding the pipeline schema. Now, the parameters can be changed as mentioned above but keep in mind that changing the parameter datatype depends on the default value specified in the `nextflow.config` file.
 
 ### Linting a pipeline schema
 
 The pipeline schema is linted as part of the main pipeline `nf-core lint` command,
 however sometimes it can be useful to quickly check the syntax of the JSONSchema without running a full lint run.
 
-Usage is `nf-core schema lint <schema>`, eg:
+Usage is `nf-core schema lint <schema>` (defaulting to `nextflow_schema.json`), eg:
 
 <!-- RICH-CODEX
 working_dir: tmp/nf-core-nextbigthing
 -->
 
-![`nf-core schema lint nextflow_schema.json`](docs/images/nf-core-schema-lint.svg)
+![`nf-core schema lint`](docs/images/nf-core-schema-lint.svg)
 
 ## Bumping a pipeline version number
 
@@ -1030,6 +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
 -->
 
@@ -1043,6 +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)
@@ -1054,6 +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)
@@ -1073,6 +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)
@@ -1132,6 +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)
@@ -1160,10 +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
 
@@ -1175,6 +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)
@@ -1190,6 +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)

docs/api/_src/pipeline_lint_tests/system_exit.md

@@ -0,0 +1,5 @@
+# system_exit
+
+```{eval-rst}
+.. automethod:: nf_core.lint.PipelineLint.system_exit
+```