Merge pull request #534 from nf-core/dev

Dev > Master for 3.0 release

.github/CONTRIBUTING.md

@@ -18,8 +18,9 @@ If you'd like to write some code for nf-core/rnaseq, the standard workflow is as
 1. Check that there isn't already an issue about your idea in the [nf-core/rnaseq issues](https://github.com/nf-core/rnaseq/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/rnaseq repository](https://github.com/nf-core/rnaseq) 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/rnaseq documentation](https://nf-co.re/rnaseq/usage) and don't hesitate to get in touch on the nf-core Slack [#rnaseq](https://nfcore.slack.com/channels/rnaseq) channel ([join our Slack here](https://nf-co.re/join/slack)).
+
+## Pipeline contribution conventions
+
+To make the nf-core/rnaseq 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

@@ -1,13 +1,25 @@
+---
+name: Bug report
+about: Report something that is broken or incorrect
+labels: bug
+---
+
 <!--
 # nf-core/rnaseq 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:
+
+- [ ] [nf-core website: troubleshooting](https://nf-co.re/usage/troubleshooting)
+- [ ] [nf-core/rnaseq pipeline documentation](https://nf-co.re/nf-core/rnaseq/usage)
+
 ## Description of the bug
 
 <!-- A clear and concise description of what the bug is. -->
@@ -23,6 +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/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 #rnaseq channel"
+    url: https://nfcore.slack.com/channels/rnaseq
+    about: Discussion about the nf-core/rnaseq pipeline

.github/ISSUE_TEMPLATE/feature_request.md

@@ -1,3 +1,9 @@
+---
+name: Feature request
+about: Suggest an idea for the nf-core website
+labels: enhancement
+---
+
 <!--
 # nf-core/rnaseq feature request
 

.github/PULL_REQUEST_TEMPLATE.md

@@ -13,9 +13,13 @@ Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/rnas
 
 ## PR checklist
 
-- [ ] PR is to `dev` rather than `master`
-- [ ] 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/rnaseq branch on the nf-core/test-datasets repo](https://github.com/nf-core/test-datasets/pull/new/nf-core/rnaseq)
+ - [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/rnaseq/tree/master/.github/CONTRIBUTING.md)
+ - [ ] If necessary, also make a PR on the nf-core/rnaseq _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

@@ -1,7 +1,12 @@
 # Markdownlint configuration file
-default: true,
+default: true
 line-length: false
 no-duplicate-header:
     siblings_only: true
-MD033:
-    allowed_elements: [details, summary, p, img]
+no-inline-html:
+    allowed_elements:
+        - img
+        - p
+        - kbd
+        - details
+        - summary

.github/workflows/awsfulltest.yml

@@ -4,8 +4,9 @@ name: nf-core AWS full size tests
 # It runs the -profile 'test_full' on AWS batch
 
 on:
-  release:
-    types: [published]
+  workflow_run:
+    workflows: ["nf-core Docker push (release)"]
+    types: [completed]
   workflow_dispatch:
 
 jobs:
@@ -15,7 +16,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Setup Miniconda
-        uses: goanpeca/setup-miniconda@v1.0.2
+        uses: conda-incubator/setup-miniconda@v2
         with:
           auto-update-conda: true
           python-version: 3.7

.github/workflows/awstest.yml

@@ -13,7 +13,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Setup Miniconda
-        uses: goanpeca/setup-miniconda@v1.0.2
+        uses: conda-incubator/setup-miniconda@v2
         with:
           auto-update-conda: true
           python-version: 3.7

.github/workflows/branch.yml

@@ -2,7 +2,7 @@ name: nf-core branch protection
 # This workflow is triggered on PRs to master branch on the repository
 # It fails when someone tries to make a PR against the nf-core `master` branch instead of `dev`
 on:
-  pull_request:
+  pull_request_target:
     branches: [master]
 
 jobs:

.github/workflows/ci.yml

@@ -20,7 +20,7 @@ jobs:
     strategy:
       matrix:
         # Nextflow versions: check pipeline minimum and current latest
-        nxf_ver: ['20.07.1', '']
+        nxf_ver: ['20.11.0-edge']
     steps:
       - name: Check out pipeline code
         uses: actions/checkout@v2
@@ -34,12 +34,12 @@ jobs:
         run: |
           nextflow run ${GITHUB_WORKSPACE} -profile test,docker
 
-  star:
-    name: Test STAR with workflow parameters
+  star_salmon:
+    name: Test STAR Salmon with workflow parameters
     if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/rnaseq') }}
     runs-on: ubuntu-latest
     env:
-      NXF_VER: '20.07.1'
+      NXF_VER: '20.11.0-edge'
       NXF_ANSI_LOG: false
     strategy:
       matrix:
@@ -49,6 +49,7 @@ jobs:
           - '--skip_trimming'
           - '--gtf false'
           - '--star_index false'
+          - '--transcript_fasta false'
           - '--min_mapped_reads 90'
           - '--with_umi'
           - '--with_umi --skip_trimming'
@@ -63,14 +64,14 @@ jobs:
 
       - name: Run pipeline with STAR and various parameters
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --aligner star ${{ matrix.parameters }}
+          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --aligner star_salmon ${{ matrix.parameters }}
 
   star_rsem:
     name: Test STAR RSEM with workflow parameters
     if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/rnaseq') }}
     runs-on: ubuntu-latest
     env:
-      NXF_VER: '20.07.1'
+      NXF_VER: '20.11.0-edge'
       NXF_ANSI_LOG: false
     strategy:
       matrix:
@@ -82,6 +83,8 @@ jobs:
         uses: actions/checkout@v2
 
       - name: Install Nextflow
+        env:
+          CAPSULE_LOG: none
         run: |
           wget -qO- get.nextflow.io | bash
           sudo mv nextflow /usr/local/bin/
@@ -95,7 +98,7 @@ jobs:
     if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/rnaseq') }}
     runs-on: ubuntu-latest
     env:
-      NXF_VER: '20.07.1'
+      NXF_VER: '20.11.0-edge'
       NXF_ANSI_LOG: false
     strategy:
       matrix:
@@ -120,7 +123,7 @@ jobs:
     if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/rnaseq') }}
     runs-on: ubuntu-latest
     env:
-      NXF_VER: '20.07.1'
+      NXF_VER: '20.11.0-edge'
       NXF_ANSI_LOG: false
     strategy:
       matrix:
@@ -145,7 +148,7 @@ jobs:
     if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/rnaseq') }}
     runs-on: ubuntu-latest
     env:
-      NXF_VER: '20.07.1'
+      NXF_VER: '20.11.0-edge'
       NXF_ANSI_LOG: false
     steps:
       - name: Check out pipeline code

.github/workflows/linting.yml

@@ -41,6 +41,8 @@ jobs:
         uses: actions/checkout@v2
 
       - name: Install Nextflow
+        env:
+          CAPSULE_LOG: none
         run: |
           wget -qO- get.nextflow.io | bash
           sudo mv nextflow /usr/local/bin/
@@ -60,12 +62,19 @@ jobs:
           GITHUB_COMMENTS_URL: ${{ github.event.pull_request.comments_url }}
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           GITHUB_PR_COMMIT: ${{ github.event.pull_request.head.sha }}
-        run: nf-core -l lint_log.txt lint ${GITHUB_WORKSPACE}
+        run: nf-core -l lint_log.txt lint ${GITHUB_WORKSPACE} --markdown lint_results.md
+
+      - name: Save PR number
+        if: ${{ always() }}
+        run: echo ${{ github.event.pull_request.number }} > PR_number.txt
 
       - name: Upload linting log file artifact
         if: ${{ always() }}
         uses: actions/upload-artifact@v2
         with:
           name: linting-log-file
-          path: lint_log.txt
+          path: |
+            lint_log.txt
+            lint_results.md
+            PR_number.txt
 

.github/workflows/linting_comment.yml

@@ -0,0 +1,29 @@
+
+name: nf-core linting comment
+# This workflow is triggered after the linting action is complete
+# It posts an automated comment to the PR, even if the PR is coming from a fork
+
+on:
+  workflow_run:
+    workflows: ["nf-core linting"]
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Download lint results
+        uses: dawidd6/action-download-artifact@v2
+        with:
+          workflow: linting.yml
+
+      - name: Get PR number
+        id: pr_number
+        run: echo "::set-output name=pr_number::$(cat linting-logs/PR_number.txt)"
+
+      - name: Post PR comment
+        uses: marocchino/sticky-pull-request-comment@v2
+        with:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          number: ${{ steps.pr_number.outputs.pr_number }}
+          path: linting-logs/lint_results.md
+