Merge pull request #2 from nf-core/master

Merge from base

.circleci/config.yml

@@ -6,7 +6,7 @@ jobs:
     environment:
       GENOME: GRCh37
       SNPEFF_CACHE_VERSION: "75"
-      SAREK_TAG: "2.6.1"
+      SAREK_TAG: 2.7
     steps:
       - checkout
       - setup_remote_docker
@@ -20,28 +20,28 @@ jobs:
     environment:
       GENOME: GRCh38
       SNPEFF_CACHE_VERSION: "86"
-      SAREK_TAG: "2.6.1"
+      SAREK_TAG: 2.7
 
   snpeffgrcm38:
     << : *buildsnpeff
     environment:
       GENOME: GRCm38
       SNPEFF_CACHE_VERSION: "86"
-      SAREK_TAG: "2.6.1"
+      SAREK_TAG: 2.7
 
   snpeffcanfam3_1:
     << : *buildsnpeff
     environment:
       GENOME: CanFam3.1
       SNPEFF_CACHE_VERSION: "86"
-      SAREK_TAG: "2.6.1"
+      SAREK_TAG: 2.7
 
   snpeffwbcel235:
     << : *buildsnpeff
     environment:
       GENOME: WBcel235
       SNPEFF_CACHE_VERSION: "86"
-      SAREK_TAG: "2.6.1"
+      SAREK_TAG: 2.7
 
   vepgrch37: &buildvep
     docker:
@@ -50,7 +50,7 @@ jobs:
       GENOME: GRCh37
       SPECIES: homo_sapiens
       VEP_VERSION: "99"
-      SAREK_TAG: "2.6.1"
+      SAREK_TAG: 2.7
     steps:
       - checkout
       - setup_remote_docker
@@ -67,31 +67,31 @@ jobs:
       GENOME: GRCh38
       SPECIES: homo_sapiens
       VEP_VERSION: "99"
-      SAREK_TAG: "2.6.1"
+      SAREK_TAG: 2.7
 
   vepgrcm38:
     << : *buildvep
     environment:
       GENOME: GRCm38
       SPECIES: mus_musculus
       VEP_VERSION: "99"
-      SAREK_TAG: "2.6.1"
+      SAREK_TAG: 2.7
 
   vepcanfam3_1:
     << : *buildvep
     environment:
       GENOME: CanFam3.1
       SPECIES: canis_familiaris
       VEP_VERSION: "99"
-      SAREK_TAG: "2.6.1"
+      SAREK_TAG: 2.7
 
   vepwbcel235:
     << : *buildvep
     environment:
       GENOME: WBcel235
       SPECIES: caenorhabditis_elegans
       VEP_VERSION: "99"
-      SAREK_TAG: "2.6.1"
+      SAREK_TAG: 2.7
 
 workflows:
   version: 2

.github/.dockstore.yml

@@ -0,0 +1,5 @@
+# Dockstore config version, not pipeline version
+version: 1.2
+workflows:
+  - subclass: nfl
+    primaryDescriptorPath: /nextflow.config

.github/CONTRIBUTING.md

@@ -18,8 +18,9 @@ If you'd like to write some code for nf-core/sarek, the standard workflow is as
 1. Check that there isn't already an issue about your idea in the [nf-core/sarek issues](https://github.com/nf-core/sarek/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/sarek repository](https://github.com/nf-core/sarek) 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 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/).
 
@@ -30,14 +31,14 @@ 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.
 `GitHub Actions` then runs the pipeline on this data to ensure that it exits successfully.
@@ -46,12 +47,82 @@ 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.
 
 ## Getting help
 
-For further information/help, please consult the [nf-core/sarek documentation](https://nf-co.re/sarek/docs) and don't hesitate to get in touch on the nf-core Slack [#sarek](https://nfcore.slack.com/channels/sarek) channel ([join our Slack here](https://nf-co.re/join/slack)).
+For further information/help, please consult the [nf-core/sarek documentation](https://nf-co.re/sarek/usage) and don't hesitate to get in touch on the nf-core Slack [#sarek](https://nfcore.slack.com/channels/sarek) channel ([join our Slack here](https://nf-co.re/join/slack)).
+
+## Pipeline contribution conventions
+
+To make the nf-core/sarek 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 flags/options to `nextflow.config` with a default (see below).
+5. Add any new flags/options to `nextflow_schema.json` with help text (with `nf-core schema build .`)
+6. Add any new flags/options to the help message (for integer/text parameters, print to help the corresponding `nextflow.config` parameter).
+7. Add sanity checks for all relevant parameters.
+8. Add any new software to the `scrape_software_versions.py` script in `bin/` and the version command to the `scrape_software_versions` process in `main.nf`.
+9. Do local tests that the new code works properly and as expected.
+10. Add a new test command in `.github/workflow/ci.yaml`.
+11. If applicable add a [MultiQC](https://https://multiqc.info/) module.
+12. Update MultiQC config `assets/multiqc_config.yaml` so relevant suffixes, name clean up, General Statistics Table column order, and module figures are in the right order.
+13. Optional: Add any descriptions of MultiQC report sections and output files 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 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/master/nf_core/pipeline-template/%7B%7Bcookiecutter.name_noslash%7D%7D/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 `${task.cpu}` and `${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 bump-version --nextflow . [min-nf-version]`
+
+### Software version reporting
+
+If you add a new tool to the pipeline, please ensure you add the information of the tool to the `get_software_version` process.
+
+Add to the script block of the process, something like the following:
+
+```bash
+<YOUR_TOOL> --version &> v_<YOUR_TOOL>.txt 2>&1 || true
+```
+
+or
+
+```bash
+<YOUR_TOOL> --help | head -n 1 &> v_<YOUR_TOOL>.txt 2>&1 || true
+```
+
+You then need to edit the script `bin/scrape_software_versions.py` to:
+
+1. Add a Python regex for your tool's `--version` output (as in stored in the `v_<YOUR_TOOL>.txt` file), to ensure the version is reported as a `v` and the version number e.g. `v2.1.1`
+2. Add a HTML entry to the `OrderedDict` for formatting in MultiQC.
+
+### 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/ISSUE_TEMPLATE/bug_report.md

@@ -1,24 +1,49 @@
+---
+name: Bug report
+about: Report something that is broken or incorrect
+title: "[BUG]"
+labels: bug
+assignees: MaxUlysse
+
+---
+
+<!--
 # nf-core/sarek bug report
 
 Hi there!
 
 Thanks for telling us about a problem with the pipeline.
 Please delete this text and anything that's not relevant from the template below:
+-->
+
+## Check Documentation
+
+I have checked the following places for your error:
 
-## Describe the bug
+- [ ] [nf-core website: troubleshooting](https://nf-co.re/usage/troubleshooting)
+- [ ] [nf-core/sarek pipeline documentation](https://nf-co.re/nf-core/sarek/usage)
 
-A clear and concise description of what the bug is.
+## Description of the bug
+
+<!-- A clear and concise description of what the bug is. -->
 
 ## Steps to reproduce
 
 Steps to reproduce the behaviour:
 
-1. Command line: `nextflow run ...`
-2. See error: _Please provide your error message_
+1. Command line: <!-- [e.g. `nextflow run ...`] -->
+2. See error: <!-- [Please provide your error message] -->
 
 ## Expected behaviour
 
-A clear and concise description of what you expected to happen.
+<!-- A clear and concise description of what you expected to happen. -->
+
+## Log files
+
+Have you provided the following extra information/files:
+
+- [ ] The command used to run the pipeline
+- [ ] The `.nextflow.log` file <!-- this is a hidden file in the directory where you launched the pipeline -->
 
 ## System
 
@@ -33,10 +58,10 @@ A clear and concise description of what you expected to happen.
 
 ## Container engine
 
-- Engine: <!-- [e.g. Conda, Docker or Singularity] -->
+- Engine: <!-- [e.g. Conda, Docker, Singularity or Podman] -->
 - version: <!-- [e.g. 1.0.0] -->
 - Image tag: <!-- [e.g. nfcore/sarek:2.6] -->
 
 ## Additional context
 
-Add any other context about the problem here.
+<!-- Add any other context about the problem here. -->

.github/ISSUE_TEMPLATE/config.yml

@@ -0,0 +1,8 @@
+blank_issues_enabled: false
+contact_links:
+  - name: Join nf-core
+    url: https://nf-co.re/join
+    about: Please join the nf-core community here
+  - name: "Slack #sarek channel"
+    url: https://nfcore.slack.com/channels/sarek
+    about: Discussion about the nf-core/sarek pipeline

.github/ISSUE_TEMPLATE/feature_request.md

@@ -1,24 +1,35 @@
+---
+name: Feature request
+about: Suggest an idea for the nf-core/sarek pipeline
+title: "[FEATURE]"
+labels: enhancement
+assignees: MaxUlysse
+
+---
+
+<!--
 # nf-core/sarek feature request
 
 Hi there!
 
 Thanks for suggesting a new feature for the pipeline!
 Please delete this text and anything that's not relevant from the template below:
+-->
 
 ## Is your feature request related to a problem? Please describe
 
-A clear and concise description of what the problem is.
+<!-- A clear and concise description of what the problem is. -->
 
-Ex. I'm always frustrated when [...]
+<!-- e.g. [I'm always frustrated when ...] -->
 
 ## Describe the solution you'd like
 
-A clear and concise description of what you want to happen.
+<!-- A clear and concise description of what you want to happen. -->
 
 ## Describe alternatives you've considered
 
-A clear and concise description of any alternative solutions or features you've considered.
+<!-- A clear and concise description of any alternative solutions or features you've considered. -->
 
 ## Additional context
 
-Add any other context about the feature request here.
+<!-- Add any other context about the feature request here. -->

.github/PULL_REQUEST_TEMPLATE.md

@@ -1,19 +1,26 @@
+<!--
 # nf-core/sarek pull request
 
 Many thanks for contributing to nf-core/sarek!
 
 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/sarek/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/sarek branch on the nf-core/test-datasets repo](https://github.com/nf-core/test-datasets/pull/new/nf-core/sarek)
-- [ ] Ensure the test suite passes (`nextflow run . -profile test,docker`).
+  - [ ] If you've added a new tool - add to the software_versions process and a regex to `scrape_software_versions.py`
+  - [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/sarek/tree/master/.github/CONTRIBUTING.md)
+  - [ ] If necessary, also make a PR on the nf-core/sarek _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository.
 - [ ] 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/sarek/tree/master/.github/CONTRIBUTING.md)
+- [ ] Ensure the test suite passes (`nextflow run . -profile test,docker`).
+- [ ] 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).

.github/RELEASE_CHECKLIST.md

@@ -27,7 +27,7 @@
 7. Wait for reviews
 8. Merge said PR
 9. Make a [release](https://github.com/nf-core/sarek/releases) on GitHub
-10. Update [bio.tools](https://bio.tools/Sarek) with the new release details
+10. Update [bio.tools](https://bio.tools/nf-core-sarek) with the new release details
 11. RT the nf-core automated tweet about the new released version
 12. Make a new branch from `dev`
 13. Checkout the `CHANGELOG.md` from `master`

.github/markdownlint.yml

@@ -1,10 +1,13 @@
 # Markdownlint configuration file
-default: true,
+default: true
 line-length: false
 no-duplicate-header:
     siblings_only: true
-no-inline-html: 
+no-inline-html:
     allowed_elements:
         - a
+        - details
         - img
-        - p
+        - kbd
+        - p
+        - summary