Phaseimpute template update and pass first test

.editorconfig

@@ -35,3 +35,9 @@ indent_style = unset
 # ignore python
 [*.{py,md}]
 indent_style = unset
+
+[/docs/*.xml]
+indent_style = unset
+
+[/docs/images/metro/*.xml]
+indent_style = unset

.github/CONTRIBUTING.md

@@ -16,15 +16,11 @@ Contributions to the code are even more welcome ;)
 
 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
 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 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
-3. Make the necessary changes / additions within your forked repository following [Pipeline conventions](#pipeline-contribution-conventions)
-4. Use `nf-core 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/).
 
@@ -41,15 +37,13 @@ Typically, pull-requests are only fully reviewed when these tests are passing, t
 
 There are typically two types of tests that run:
 
-### Lint tests
 ### 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 lint <pipeline-directory>` command.
 
 If any failures or warnings are encountered, please follow the listed URL for more documentation.
 
-### Pipeline tests
 ### Pipeline tests
 
 Each `nf-core` pipeline should be set up with a minimal set of test-data.
@@ -59,7 +53,6 @@ These tests are run both with the latest available version of `Nextflow` and als
 
 ## Patch
 
-:warning: Only in the unlikely and regretful event of a release happening with a bug.
 :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/master`.

.github/PULL_REQUEST_TEMPLATE.md

@@ -1,5 +1,4 @@
 <!--
-<!--
 # nf-core/phaseimpute pull request
 
 Many thanks for contributing to nf-core/phaseimpute!
@@ -12,14 +11,8 @@ Remember that PRs should be made against the dev branch, unless you're preparing
 Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/phaseimpute/tree/master/.github/CONTRIBUTING.md)
 -->
 
-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/master/.github/CONTRIBUTING.md)
--->
-
 ## PR checklist
 
-- [ ] This comment contains a description of changes (with reason).
 - [ ] 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/master/.github/CONTRIBUTING.md)

.github/workflows/branch.yml

@@ -4,18 +4,13 @@ name: nf-core branch protection
 on:
   pull_request_target:
     branches: [master]
-  pull_request_target:
-    branches: [master]
 
 jobs:
   test:
-    runs-on: ubuntu-latest
     runs-on: ubuntu-latest
     steps:
-      # PRs to the nf-core repo master branch are only ok if coming from the nf-core repo `dev` or any `patch` branches
       # PRs to the nf-core repo master branch are only ok if coming from the nf-core repo `dev` or any `patch` branches
       - name: Check PRs
-        if: github.repository == 'nf-core/phaseimpute'
         if: github.repository == 'nf-core/phaseimpute'
         run: |
           { [[ ${{github.event.pull_request.head.repo.full_name }} == nf-core/phaseimpute ]] && [[ $GITHUB_HEAD_REF == "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]]

.github/workflows/ci.yml

@@ -32,9 +32,6 @@ concurrency:
 
 jobs:
   test:
-    name: Run pipeline with test data
-    # Only run on push if this is the nf-core dev branch (merged PRs)
-    if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/phaseimpute') }}"
     name: Run pipeline with test data
     # Only run on push if this is the nf-core dev branch (merged PRs)
     if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/phaseimpute') }}"
@@ -44,9 +41,6 @@ jobs:
         NXF_VER:
           - "23.04.0"
           - "latest-everything"
-        NXF_VER:
-          - "23.04.0"
-          - "latest-everything"
     steps:
       - name: Check out pipeline code
         uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4

.github/workflows/linting.yml

@@ -2,14 +2,10 @@ name: nf-core linting
 # This workflow is triggered on pushes and PRs to the repository.
 # It runs the `nf-core lint` and markdown lint tests to ensure
 # that the code meets the nf-core guidelines.
-# It runs the `nf-core lint` and markdown lint tests to ensure
-# that the code meets the nf-core guidelines.
 on:
   push:
     branches:
       - dev
-    branches:
-      - dev
   pull_request:
   release:
     types: [published]
@@ -51,7 +47,6 @@ jobs:
           python -m pip install --upgrade pip
           pip install nf-core
 
-
       - name: Run nf-core lint
         env:
           GITHUB_COMMENTS_URL: ${{ github.event.pull_request.comments_url }}

.gitignore

@@ -6,4 +6,5 @@ results/
 testing/
 testing*
 *.pyc
-*.code-workspace
+*.code-workspace
+.nf-test*

CODE_OF_CONDUCT.md

@@ -45,10 +45,8 @@ Questions, concerns, or ideas on what we can include? Contact members of the Saf
 ## Our Responsibilities
 
 Members of the Safety Team (the Safety Officers) are responsible for clarifying the standards of acceptable behavior and are expected to take appropriate and fair corrective action in response to any instances of unacceptable behaviour.
-The safety officer is responsible for clarifying the standards of acceptable behavior and are expected to take appropriate and fair corrective action in response to any instances of unacceptable behaviour.
 
 The Safety Team, in consultation with the nf-core core team, have the right and responsibility to remove, edit, or reject comments, commits, code, wiki edits, issues, and other contributions that are not aligned to this CoC, or to ban temporarily or permanently any contributor for other behaviors that they deem inappropriate, threatening, offensive, or harmful.
-The safety officer in consultation with the nf-core core team have the right and responsibility to remove, edit, or reject comments, commits, code, wiki edits, issues, and other contributions that are not aligned to this Code of Conduct, or to ban temporarily or permanently any contributor for other behaviors that they deem inappropriate, threatening, offensive, or harmful.
 
 Members of the core team or the Safety Team who violate the CoC will be required to recuse themselves pending investigation. They will not have access to any reports of the violations and will be subject to the same actions as others in violation of the CoC.