Merge pull request #152 from nf-core/dev

Release 1.2.0

.github/CONTRIBUTING.md

@@ -18,8 +18,9 @@ If you'd like to write some code for nf-core/mag, the standard workflow is as fo
 1. Check that there isn't already an issue about your idea in the [nf-core/mag issues](https://github.com/nf-core/mag/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/mag repository](https://github.com/nf-core/mag) 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.
@@ -55,3 +56,73 @@ These tests are run both with the latest available version of `Nextflow` and als
 ## Getting help
 
 For further information/help, please consult the [nf-core/mag documentation](https://nf-co.re/mag/usage) and don't hesitate to get in touch on the nf-core Slack [#mag](https://nfcore.slack.com/channels/mag) channel ([join our Slack here](https://nf-co.re/join/slack)).
+
+## Pipeline contribution conventions
+
+To make the nf-core/mag 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

@@ -13,6 +13,13 @@ 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:
+
+- [ ] [nf-core website: troubleshooting](https://nf-co.re/usage/troubleshooting)
+- [ ] [nf-core/mag pipeline documentation](https://nf-co.re/nf-core/mag/usage)
+
 ## Description of the bug
 
 <!-- A clear and concise description of what the bug is. -->
@@ -28,6 +35,13 @@ Steps to reproduce the behaviour:
 
 <!-- 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
 
 - Hardware: <!-- [e.g. HPC, Desktop, Cloud...] -->

.github/PULL_REQUEST_TEMPLATE.md

@@ -13,8 +13,14 @@ Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/mag/
 
 ## PR checklist
 
-- [ ] This comment contains a description of changes (with reason)
-- [ ] `CHANGELOG.md` is updated
+- [ ] This comment contains a description of changes (with reason).
 - [ ] If you've fixed a bug or added code that should be tested, add tests!
-- [ ] Documentation in `docs` is updated
-- [ ] If necessary, also make a PR on the [nf-core/mag branch on the nf-core/test-datasets repo](https://github.com/nf-core/test-datasets/pull/new/nf-core/mag)
+ - [ ] 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/mag/tree/master/.github/CONTRIBUTING.md)
+ - [ ] If necessary, also make a PR on the nf-core/mag _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 +1,12 @@
 # Markdownlint configuration file
-default: true,
+default: true
 line-length: false
 no-duplicate-header:
     siblings_only: true
 no-inline-html:
     allowed_elements:
         - img
         - p
+        - kbd
+        - details
+        - summary

.github/workflows/ci.yml

@@ -34,13 +34,13 @@ jobs:
 
       - name: Build new docker image
         if: env.MATCHED_FILES
-        run: docker build --no-cache . -t nfcore/mag:1.1.2
+        run: docker build --no-cache . -t nfcore/mag:1.2.0
 
       - name: Pull docker image
         if: ${{ !env.MATCHED_FILES }}
         run: |
           docker pull nfcore/mag:dev
-          docker tag nfcore/mag:dev nfcore/mag:1.1.2
+          docker tag nfcore/mag:dev nfcore/mag:1.2.0
 
       - name: Check if BUSCO Dockerfile or Conda environment changed
         uses: technote-space/get-diff-action@v4
@@ -51,13 +51,13 @@ jobs:
 
       - name: Build new docker image for BUSCO
         if: env.MATCHED_FILES
-        run: docker build --no-cache ./containers/busco/ -t nfcore/magbusco:1.1.2
+        run: docker build --no-cache ./containers/busco/ -t nfcore/magbusco:1.2.0
 
       - name: Pull docker image for BUSCO
         if: ${{ !env.MATCHED_FILES }}
         run: |
           docker pull nfcore/magbusco:dev
-          docker tag nfcore/magbusco:dev nfcore/magbusco:1.1.2
+          docker tag nfcore/magbusco:dev nfcore/magbusco:1.2.0
 
       - name: Install Nextflow
         env:

CHANGELOG.md

@@ -3,6 +3,26 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## v1.2.0 - 2020/02/10
+
+### `Added`
+
+- [#146](https://github.com/nf-core/mag/pull/146) - Add `--coassemble_group` parameter to allow group-wise co-assembly
+- [#146](https://github.com/nf-core/mag/pull/146) - Add `--binning_map_mode` parameter allowing different mapping strategies to compute co-abundances used for binning (`all`, `group`, `own`)
+- [#149](https://github.com/nf-core/mag/pull/149) - Add two new parameters to allow custom SPAdes and MEGAHIT options (`--spades_options` and `--megahit_options`)
+
+### `Changed`
+
+- [#141](https://github.com/nf-core/mag/pull/141) - Update to nf-core 1.12.1 `TEMPLATE`
+- [#143](https://github.com/nf-core/mag/pull/143) - Manifest file has to be handed over via `--input` parameter now
+- [#143](https://github.com/nf-core/mag/pull/143) - Changed format of manifest input file: requires a '.tsv' suffix and additionally contains group ID
+- [#143](https://github.com/nf-core/mag/pull/143) - TSV `--input` file allows now also entries containing only short reads
+- [#145](https://github.com/nf-core/mag/pull/145) - When using TSV input files, uses sample IDs now for `FastQC` instead of basenames of original read files. Allows non-unique file basenames.
+
+### `Deprecated`
+
+- [#143](https://github.com/nf-core/mag/pull/143) - Change depreciated parameters: `--manifest` -> `--input`
+
 ## v1.1.2 - 2020/11/24
 
 ### `Changed`

Dockerfile

@@ -1,4 +1,4 @@
-FROM nfcore/base:1.12
+FROM nfcore/base:1.12.1
 LABEL authors="Hadrien Gourlé <[email protected]>, Daniel Straub <[email protected]>, Sabrina Krakau <[email protected]>" \
       description="Docker image containing all software requirements for the nf-core/mag pipeline"
 
@@ -7,10 +7,10 @@ COPY environment.yml /
 RUN conda env create --quiet -f /environment.yml && conda clean -a
 
 # Add conda installation dir to PATH (instead of doing 'conda activate')
-ENV PATH /opt/conda/envs/nf-core-mag-1.1.2/bin:$PATH
+ENV PATH /opt/conda/envs/nf-core-mag-1.2.0/bin:$PATH
 
 # Dump the details of the installed packages to a file for posterity
-RUN conda env export --name nf-core-mag-1.1.2 > nf-core-mag-1.1.2.yml
+RUN conda env export --name nf-core-mag-1.2.0 > nf-core-mag-1.2.0.yml
 
 # Instruct R processes to use these empty files instead of clashing with a local version
 RUN touch .Rprofile