phaseimpute first release (v1.0.0)

.devcontainer/devcontainer.json

@@ -0,0 +1,20 @@
+{
+    "name": "nfcore",
+    "image": "nfcore/gitpod:latest",
+    "remoteUser": "gitpod",
+    "runArgs": ["--privileged"],
+
+    // Configure tool-specific properties.
+    "customizations": {
+        // Configure properties specific to VS Code.
+        "vscode": {
+            // Set *default* container specific settings.json values on container create.
+            "settings": {
+                "python.defaultInterpreterPath": "/opt/conda/bin/python"
+            },
+
+            // Add the IDs of extensions you want installed when the container is created.
+            "extensions": ["ms-python.python", "ms-python.vscode-pylance", "nf-core.nf-core-extensionpack"]
+        }
+    }
+}

.editorconfig

@@ -0,0 +1,42 @@
+root = true
+
+[*]
+charset = utf-8
+end_of_line = lf
+insert_final_newline = true
+trim_trailing_whitespace = true
+indent_size = 4
+indent_style = space
+
+[*.{md,yml,yaml,html,css,scss,js}]
+indent_size = 2
+
+# These files are edited and tested upstream in nf-core/modules
+[/modules/nf-core/**]
+charset = unset
+end_of_line = unset
+insert_final_newline = unset
+trim_trailing_whitespace = unset
+indent_style = unset
+[/subworkflows/nf-core/**]
+charset = unset
+end_of_line = unset
+insert_final_newline = unset
+trim_trailing_whitespace = unset
+indent_style = unset
+
+[/assets/email*]
+indent_size = unset
+
+# ignore python and markdown
+[*.{py,md}]
+indent_style = unset
+
+[/docs/*.xml*]
+indent_style = unset
+insert_final_newline = unset
+
+[/docs/images/metro/*.xml*]
+indent_style = unset
+insert_final_newline = unset
+end_of_line = unset

.gitattributes

@@ -1 +1,4 @@
 *.config linguist-language=nextflow
+*.nf.test linguist-language=nextflow
+modules/nf-core/** linguist-generated
+subworkflows/nf-core/** linguist-generated

.github/.dockstore.yml

@@ -0,0 +1,6 @@
+# Dockstore config version, not pipeline version
+version: 1.2
+workflows:
+  - subclass: nfl
+    primaryDescriptorPath: /nextflow.config
+    publish: True

.github/CONTRIBUTING.md

@@ -9,35 +9,42 @@ Please use the pre-filled template to save time.
 However, don't be put off by this template - other more general issues and suggestions are welcome!
 Contributions to the code are even more welcome ;)
 
+> [!NOTE]
 > If you need help using or modifying nf-core/phaseimpute then the best place to ask is on the nf-core Slack [#phaseimpute](https://nfcore.slack.com/channels/phaseimpute) channel ([join our Slack here](https://nf-co.re/join/slack)).
 
 ## Contribution workflow
 
 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
-4. 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 pipelines 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/).
 
 ## Tests
 
+You have the option to test your changes locally by running the pipeline. For receiving warnings about process selectors and other `debug` information, it is recommended to use the debug profile. Execute all the tests with the following command:
+
+```bash
+nf-test test --profile debug,test,docker --verbose
+```
+
 When you create a pull request with changes, [GitHub Actions](https://github.com/features/actions) will run automatic tests.
 Typically, pull-requests are only fully reviewed when these tests are passing, though of course we can help out before then.
 
 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.
+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 pipelines 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.
 `GitHub Actions` then runs the pipeline on this data to ensure that it exits successfully.
@@ -46,12 +53,73 @@ 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`.
-* Fix the bug, and bump version (X.Y.Z+1).
-* A PR should be made on `master` from patch to directly this particular bug.
+- On your own fork, make a new branch `patch` based on `upstream/master`.
+- Fix the bug, and bump version (X.Y.Z+1).
+- A PR should be made on `master` from patch to directly this particular bug.
 
 ## Getting help
 
-For further information/help, please consult the [nf-core/phaseimpute documentation](https://nf-co.re/nf-core/phaseimpute/docs) and don't hesitate to get in touch on the nf-core Slack [#phaseimpute](https://nfcore.slack.com/channels/phaseimpute) channel ([join our Slack here](https://nf-co.re/join/slack)).
+For further information/help, please consult the [nf-core/phaseimpute documentation](https://nf-co.re/phaseimpute/usage) and don't hesitate to get in touch on the nf-core Slack [#phaseimpute](https://nfcore.slack.com/channels/phaseimpute) channel ([join our Slack here](https://nf-co.re/join/slack)).
+
+## Pipeline contribution conventions
+
+To make the nf-core/phaseimpute code and processing logic more understandable for new contributors and to ensure quality, we semi-standardise the way the code and other contributions are written.
+
+### Adding a new step
+
+If you wish to contribute a new step, please use the following coding standards:
+
+1. Define the corresponding input channel into your new process from the expected previous process channel
+2. Write the process block (see below).
+3. Define the output channel if needed (see below).
+4. Add any new parameters to `nextflow.config` with a default (see below).
+5. Add any new parameters to `nextflow_schema.json` with help text (via the `nf-core pipelines schema build` tool).
+6. Add sanity checks and validation for all relevant parameters.
+7. Perform local tests to validate that the new code works as expected.
+8. If applicable, add a new test command in `.github/workflow/ci.yml`.
+9. Update MultiQC config `assets/multiqc_config.yml` so relevant suffixes, file name clean up and module plots are in the appropriate order. If applicable, add a [MultiQC](https://https://multiqc.info/) module.
+10. Add a description of the output files and if relevant any appropriate images from the MultiQC report to `docs/output.md`.
+
+### Default values
+
+Parameters should be initialised / defined with default values in `nextflow.config` under the `params` scope.
+
+Once there, use `nf-core pipelines schema build` to add to `nextflow_schema.json`.
+
+### Default processes resource requirements
+
+Sensible defaults for process resource requirements (CPUs / memory / time) for a process should be defined in `conf/base.config`. These should generally be specified generic with `withLabel:` selectors so they can be shared across multiple processes/steps of the pipeline. A nf-core standard set of labels that should be followed where possible can be seen in the [nf-core pipeline template](https://github.com/nf-core/tools/blob/main/nf_core/pipeline-template/conf/base.config), which has the default process as a single core-process, and then different levels of multi-core configurations for increasingly large memory requirements defined with standardised labels.
+
+The process resources can be passed on to the tool dynamically within the process with the `${task.cpus}` and `${task.memory}` variables in the `script:` block.
+
+### Naming schemes
+
+Please use the following naming schemes, to make it easy to understand what is going where.
+
+- initial process channel: `ch_output_from_<process>`
+- intermediate and terminal channels: `ch_<previousprocess>_for_<nextprocess>`
+
+### Nextflow version bumping
+
+If you are using a new feature from core Nextflow, you may bump the minimum required version of nextflow in the pipeline with: `nf-core pipelines bump-version --nextflow . [min-nf-version]`
+
+### Images and figures
+
+For overview images and other documents we follow the nf-core [style guidelines and examples](https://nf-co.re/developers/design_guidelines).
+
+## GitHub Codespaces
+
+This repo includes a devcontainer configuration which will create a GitHub Codespaces for Nextflow development! This is an online developer environment that runs in your browser, complete with VSCode and a terminal.
+
+To get started:
+
+- Open the repo in [Codespaces](https://github.com/nf-core/phaseimpute/codespaces)
+- Tools installed
+  - nf-core
+  - Nextflow
+
+Devcontainer specs:
+
+- [DevContainer config](.devcontainer/devcontainer.json)

.github/ISSUE_TEMPLATE/bug_report.yml

@@ -0,0 +1,50 @@
+name: Bug report
+description: Report something that is broken or incorrect
+labels: bug
+body:
+  - type: markdown
+    attributes:
+      value: |
+        Before you post this issue, please check the documentation:
+
+        - [nf-core website: troubleshooting](https://nf-co.re/usage/troubleshooting)
+        - [nf-core/phaseimpute pipeline documentation](https://nf-co.re/phaseimpute/usage)
+
+  - type: textarea
+    id: description
+    attributes:
+      label: Description of the bug
+      description: A clear and concise description of what the bug is.
+    validations:
+      required: true
+
+  - type: textarea
+    id: command_used
+    attributes:
+      label: Command used and terminal output
+      description: Steps to reproduce the behaviour. Please paste the command you used to launch the pipeline and the output from your terminal.
+      render: console
+      placeholder: |
+        $ nextflow run ...
+
+        Some output where something broke
+
+  - type: textarea
+    id: files
+    attributes:
+      label: Relevant files
+      description: |
+        Please drag and drop the relevant files here. Create a `.zip` archive if the extension is not allowed.
+        Your verbose log file `.nextflow.log` is often useful _(this is a hidden file in the directory where you launched the pipeline)_ as well as custom Nextflow configuration files.
+
+  - type: textarea
+    id: system
+    attributes:
+      label: System information
+      description: |
+        * Nextflow version _(eg. 23.04.0)_
+        * Hardware _(eg. HPC, Desktop, Cloud)_
+        * Executor _(eg. slurm, local, awsbatch)_
+        * Container engine: _(e.g. Docker, Singularity, Conda, Podman, Shifter, Charliecloud, or Apptainer)_
+        * OS _(eg. CentOS Linux, macOS, Linux Mint)_
+        * Version of nf-core/phaseimpute _(eg. 1.1, 1.5, 1.8.2)_

.github/ISSUE_TEMPLATE/config.yml

@@ -0,0 +1,7 @@
+contact_links:
+  - name: Join nf-core
+    url: https://nf-co.re/join
+    about: Please join the nf-core community here
+  - name: "Slack #phaseimpute channel"
+    url: https://nfcore.slack.com/channels/phaseimpute
+    about: Discussion about the nf-core/phaseimpute pipeline

.github/ISSUE_TEMPLATE/feature_request.yml

@@ -0,0 +1,11 @@
+name: Feature request
+description: Suggest an idea for the nf-core/phaseimpute pipeline
+labels: enhancement
+body:
+  - type: textarea
+    id: description
+    attributes:
+      label: Description of feature
+      description: Please describe your suggestion for a new feature. It might help to describe a problem or use case, plus any alternatives that you have considered.
+    validations:
+      required: true

.github/PULL_REQUEST_TEMPLATE.md

@@ -1,19 +1,26 @@
+<!--
 # nf-core/phaseimpute pull request
 
 Many thanks for contributing to nf-core/phaseimpute!
 
 Please fill in the appropriate checklist below (delete whatever is not relevant).
 These are the most common things requested on pull requests (PRs).
 
+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 necessary, also make a PR on the [nf-core/phaseimpute branch on the nf-core/test-datasets repo](https://github.com/nf-core/test-datasets/pull/new/nf-core/phaseimpute)
-- [ ] Ensure the test suite passes (`nextflow run . -profile test,docker`).
-- [ ] Make sure your code lints (`nf-core lint .`).
-- [ ] Documentation in `docs` is updated
-- [ ] `CHANGELOG.md` is updated
-- [ ] `README.md` is updated
-
-**Learn more about contributing:** [CONTRIBUTING.md](https://github.com/nf-core/phaseimpute/tree/master/.github/CONTRIBUTING.md)
+- [ ] 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)
+- [ ] If necessary, also make a PR on the nf-core/phaseimpute _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository.
+- [ ] Make sure your code lints (`nf-core pipelines lint`).
+- [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --outdir <OUTDIR>`).
+- [ ] Check for unexpected warnings in debug mode (`nextflow run . -profile debug,test,docker --outdir <OUTDIR>`).
+- [ ] Usage Documentation in `docs/usage.md` is updated.
+- [ ] Output Documentation in `docs/output.md` is updated.
+- [ ] `CHANGELOG.md` is updated.
+- [ ] `README.md` is updated (including new tool citations and authors/contributors).