Merge pull request #4 from nf-core/dev

Latest changes

Author: jfy133

.github/CONTRIBUTING.md

@@ -18,8 +18,8 @@ If you'd like to write some code for nf-core/eager, the standard workflow is as
 1. Check that there isn't already an issue about your idea in the [nf-core/eager issues](https://github.com/nf-core/eager/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/eager repository](https://github.com/nf-core/eager) to your GitHub account
-3. Make the necessary changes / additions within your forked repository (following [code contribution guidelines](https://github.com/nf-core/eager/blob/dev/.github/CONTRIBUTING.md))
-4. Use `nf-core schema build .` and add any new parameters to the pipeline JSON schema (requires nf-core tools >= 1.10).
+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/).
@@ -31,14 +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.
@@ -57,36 +57,80 @@ These tests are run both with the latest available version of `Nextflow` and als
 
 For further information/help, please consult the [nf-core/eager documentation](https://nf-co.re/eager/usage) and don't hesitate to get in touch on the nf-core Slack [#eager](https://nfcore.slack.com/channels/eager) channel ([join our Slack here](https://nf-co.re/join/slack)).
 
-# Code Contribution Guidelines
+## Pipeline contribution conventions
 
-To make the EAGER2 code and processing logic more understandable for new contributors, and to ensure quality. We are making an attempt to somewhat-standardise the way the code is written.
+To make the nf-core/eager 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.
 
-If you wish to contribute a new module, please use the following coding standards.
+### Adding a new step
 
-The typical workflow for adding a new module is as follows:
+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 (or re-routing block, see below).
+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 .`)
+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. Add new flags/options to 'usage' documentation under `docs/usage.md`.
-14. Add any descriptions of MultiQC report sections and output files to `docs/output.md`.
+13. Optional: Add any descriptions of MultiQC report sections and output files to `docs/output.md`.
 
-## Default Values
+### Default values
 
-Default values should go in `nextflow.config` under the `params` scope, and `nextflow_schema.json` (latter with `nf-core schema build .`)
+Parameters should be initialised / defined with default values in `nextflow.config` under the `params` scope.
 
-## Default resource processes
+Once there, use `nf-core schema build .` to add to `nextflow_schema.json`.
 
-Defining recommended 'minimum' resource requirements (CPUs/Memory) for a process should be defined in `conf/base.config`. This can be utilised within the process using `${task.cpu}` or `${task.memory}` variables in the `script:` block.
+### 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.
+
+:warning: Note that in nf-core/eager we currently have our own custom process labels, so please check `base.config`!
+
+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>`
+* skipped process output: `ch_<previousstage>_for_<skipprocess>`(this goes out of the bypass statement described above)
+
+### 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).
+
+For all internal nf-core/eager documentation images we are using the 'Kalam' font by the Indian Type Foundry and licensed under the Open Font License. It can be found for download here [here](https://fonts.google.com/specimen/Kalam).
 
 ## Process Concept
 
@@ -164,44 +208,3 @@ if (params.run_fastp) {
 }
 
  ```
-
-## Naming Schemes
-
-Please use the following naming schemes, to make it easy to understand what is going where.
-
-* process output: `ch_output_from_<process>`(this should always go into the bypass statement described above).
-* skipped process output: `ch_<previousstage>_for_<skipprocess>`(this goes out of the bypass statement described above)
-* process inputs: `ch_<previousstage>_for_<process>` (this goes into a process)
-
-## Nextflow Version Bumping
-
-If you have agreement from reviewers, you may bump the 'default' minimum version of nextflow (e.g. for testing), with `nf-core bump-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 tools --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 block entry to the `OrderedDict` for formatting in MultiQC.
-
-> If a tool does not unfortunately offer any printing of version data, you may add this 'manually' e.g. with `echo "v1.1" > v_<YOUR_TOOL>.txt`
-
-## Images and Figures
-
-For all internal nf-core/eager documentation images we are using the 'Kalam' font by the Indian Type Foundry and licensed under the Open Font License. It can be found for download here [here](https://fonts.google.com/specimen/Kalam).
-
-For the overview image we follow the nf-core [style guidelines](https://nf-co.re/developers/design_guidelines).

.github/ISSUE_TEMPLATE/bug_report.md

@@ -15,12 +15,11 @@ Please delete this text and anything that's not relevant from the template below
 
 ## Check Documentation
 
-Have you checked in the following places for your error?:
+I have checked the following places for your error:
 
-- [ ] [Frequently Asked Questions](https://github.com/nf-core/eager/blob/master/docs/usage.md#troubleshooting-and-faqs)
-      (for nf-core/eager specific information)
-- [ ] [Troubleshooting](https://nf-co.re/usage/troubleshooting)
-      (for nf-core specific information)
+- [ ] [nf-core website: troubleshooting](https://nf-co.re/usage/troubleshooting)
+- [ ] [nf-core/eager pipeline documentation](https://nf-co.re/nf-core/eager/usage)
+      - nf-core/eager FAQ/troubleshooting can be found [here](https://nf-co.re/eager/usage#troubleshooting-and-faqs)
 
 ## Description of the bug
 
@@ -39,9 +38,11 @@ Steps to reproduce the behaviour:
 
 ## Log files
 
-1. Command line: <!-- [e.g. `nextflow run ...`] -->
-2. The `.nextflow.log` file (which is a hidden file in whichever place you _ran_ the pipeline from - not necessarily in the output directory!)
-3. See error: <!-- [Please provide your error message] -->
+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 -->
+- [ ] The exact error: <!-- [Please provide your error message] -->
 
 ## System
 

.github/PULL_REQUEST_TEMPLATE.md

@@ -13,13 +13,14 @@ Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/eage
 
 ## 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/eager branch on the nf-core/test-datasets repo](https://github.com/nf-core/test-datasets/pull/new/nf-core/eager)
-- [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --paired_end`).
-- [ ] Make sure your code lints ([`nf-core lint .`](https://nf-co.re/tools)).
-- [ ] Documentation in `docs` is updated
-- [ ] `CHANGELOG.md` is updated
-- [ ] `README.md` is updated
-
-**Learn more about contributing:** [CONTRIBUTING.md](https://github.com/nf-core/eager/tree/master/.github/CONTRIBUTING.md)
+ - [ ] 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/eager/tree/master/.github/CONTRIBUTING.md)
+ - [ ] If necessary, also make a PR on the nf-core/eager _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository.
+- [ ] Make sure your code lints (`nf-core lint .`).
+- [ ] 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/markdownlint.yml

@@ -1,9 +1,9 @@
 # Markdownlint configuration file
-default: true,
+default: true
 line-length: false
 no-duplicate-header:
     siblings_only: true
-no-inline-html: 
+no-inline-html:
     allowed_elements:
         - img
         - p

CHANGELOG.md

@@ -3,19 +3,21 @@
 The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.html).
 
-## [2.2.2] - 2020-12-03
+## [2.2.2] - 2020-12-09
 
 ### `Added`
 
-- Added large scale 'stress-test' profile for AWS (using de Barros Damgaard et al. 2018's 137 ancient human genomes)
+- Added large scale 'stress-test' profile for AWS (using de Barros Damgaard et al. 2018's 137 ancient human genomes).
+  - This will now be run automatically for every release. All processed data will be available on the nf-core website: <https://nf-co.re/eager/results>
+    - You can run this yourself using `-profile test_full`
 
 ### `Fixed`
 
 - Fixed AWS full test profile.
 - [#587](https://github.com/nf-core/eager/issues/587) - Re-implemented AdapterRemovalFixPrefix for DeDup compatibility of including singletons
-- [#602](https://github.com/nf-core/eager/issues/602) - Added the newly avaliable GATK 3.5 conda package.
+- [#602](https://github.com/nf-core/eager/issues/602) - Added the newly available GATK 3.5 conda package.
 - [#610](https://github.com/nf-core/eager/issues/610) - Create bwa_index channel when specifying circularmapper as mapper
-- Updated template to nf-core/tools 1.12
+- Updated template to nf-core/tools 1.12.1
 - General documentation improvements
 
 ### `Deprecated`

Dockerfile

@@ -1,4 +1,4 @@
-FROM nfcore/base:1.12
+FROM nfcore/base:1.12.1
 LABEL authors="The nf-core/eager community" \
       description="Docker image containing all software requirements for the nf-core/eager pipeline"