Merge pull request #101 from nf-core/dev

New version 1.3.0

.github/.dockstore.yml

@@ -3,3 +3,4 @@ version: 1.2
 workflows:
   - subclass: nfl
     primaryDescriptorPath: /nextflow.config
+    publish: True

.github/CONTRIBUTING.md

@@ -9,9 +9,7 @@ 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 ;)
 
-> If you need help using or modifying nf-core/hic then the best place to ask is on the nf-core
-Slack [#hic](https://nfcore.slack.com/channels/hic) channel ([join our Slack here](https://nf-co.re/join/slack)).
-
+> If you need help using or modifying nf-core/hic then the best place to ask is on the nf-core Slack [#hic](https://nfcore.slack.com/channels/hic) channel ([join our Slack here](https://nf-co.re/join/slack)).
 
 ## Contribution workflow
 
@@ -20,8 +18,9 @@ If you'd like to write some code for nf-core/hic, the standard workflow is as fo
 1. Check that there isn't already an issue about your idea in the [nf-core/hic issues](https://github.com/nf-core/hic/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/hic repository](https://github.com/nf-core/hic) 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/).
 
@@ -32,14 +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.
@@ -55,8 +54,75 @@ These tests are run both with the latest available version of `Nextflow` and als
 * 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/hic documentation](https://nf-co.re/nf-core/hic/docs) and
-don't hesitate to get in touch on the nf-core Slack [#hic](https://nfcore.slack.com/channels/hic) channel
-([join our Slack here](https://nf-co.re/join/slack)).
 
-For further information/help, please consult the [nf-core/hic documentation](https://nf-co.re/hic/docs) and don't hesitate to get in touch on the nf-core Slack [#hic](https://nfcore.slack.com/channels/hic) channel ([join our Slack here](https://nf-co.re/join/slack)).
+For further information/help, please consult the [nf-core/hic documentation](https://nf-co.re/hic/usage) and don't hesitate to get in touch on the nf-core Slack [#hic](https://nfcore.slack.com/channels/hic) channel ([join our Slack here](https://nf-co.re/join/slack)).
+
+## Pipeline contribution conventions
+
+To make the nf-core/hic 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/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

@@ -1,3 +1,9 @@
+---
+name: Bug report
+about: Report something that is broken or incorrect
+labels: bug
+---
+
 <!--
 # nf-core/hic bug report
 
@@ -7,6 +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/hic pipeline documentation](https://nf-co.re/hic/usage)
+
 ## Description of the bug
 
 <!-- A clear and concise description of what the bug is. -->
@@ -22,6 +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...] -->
@@ -35,7 +55,7 @@ Steps to reproduce the behaviour:
 
 ## Container engine
 
-- Engine: <!-- [e.g. Conda, Docker or Singularity] -->
+- Engine: <!-- [e.g. Conda, Docker, Singularity, Podman, Shifter or Charliecloud] -->
 - version: <!-- [e.g. 1.0.0] -->
 - Image tag: <!-- [e.g. nfcore/hic:1.0.0] -->
 

.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 #hic channel"
+    url: https://nfcore.slack.com/channels/hic
+    about: Discussion about the nf-core/hic pipeline

.github/ISSUE_TEMPLATE/feature_request.md

@@ -1,11 +1,16 @@
+---
+name: Feature request
+about: Suggest an idea for the nf-core/hic pipeline
+labels: enhancement
+---
+
 <!--
 # nf-core/hic 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
@@ -25,4 +30,3 @@ Please delete this text and anything that's not relevant from the template below
 ## Additional context
 
 <!-- Add any other context about the feature request here. -->
-

.github/PULL_REQUEST_TEMPLATE.md

@@ -10,12 +10,18 @@ Remember that PRs should be made against the dev branch, unless you're preparing
 
 Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/hic/tree/master/.github/CONTRIBUTING.md)
 -->
+<!-- markdownlint-disable ul-indent -->
 
 ## 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/hic branch on the nf-core/test-datasets repo](https://github.com/nf-core/test-datasets/pull/new/nf-core/hic)
-
+    - [ ] 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/hic/tree/master/.github/CONTRIBUTING.md)
+    - [ ] If necessary, also make a PR on the nf-core/hic _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

@@ -1,5 +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/awsfulltest.yml

@@ -1,10 +1,23 @@
 name: nf-core AWS full size tests
-# This workflow is triggered on push to the master branch.
+# This workflow is triggered on published releases.
+# It can be additionally triggered manually with GitHub actions workflow dispatch.
 # 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:
+
+
+env:
+  AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }}
+  AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }}
+  TOWER_ACCESS_TOKEN: ${{ secrets.AWS_TOWER_TOKEN }}
+  AWS_JOB_DEFINITION: ${{ secrets.AWS_JOB_DEFINITION }}
+  AWS_JOB_QUEUE: ${{ secrets.AWS_JOB_QUEUE }}
+  AWS_S3_BUCKET: ${{ secrets.AWS_S3_BUCKET }}
+
 
 jobs:
   run-awstest:
@@ -13,7 +26,7 @@ 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
@@ -23,13 +36,6 @@ jobs:
         # Add full size test data (but still relatively small datasets for few samples)
         # on the `test_full.config` test runs with only one set of parameters
         # Then specify `-profile test_full` instead of `-profile test` on the AWS batch command
-        env:
-          AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }}
-          AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }}
-          TOWER_ACCESS_TOKEN: ${{ secrets.AWS_TOWER_TOKEN }}
-          AWS_JOB_DEFINITION: ${{ secrets.AWS_JOB_DEFINITION }}
-          AWS_JOB_QUEUE: ${{ secrets.AWS_JOB_QUEUE }}
-          AWS_S3_BUCKET: ${{ secrets.AWS_S3_BUCKET }}
         run: |
           aws batch submit-job \
             --region eu-west-1 \

.github/workflows/awstest.yml

@@ -1,11 +1,20 @@
 name: nf-core AWS test
 # This workflow is triggered on push to the master branch.
-# It runs the -profile 'test' on AWS batch
+# It can be additionally triggered manually with GitHub actions workflow dispatch.
+# It runs the -profile 'test' on AWS batch.
 
 on:
-  push:
-    branches:
-      - master
+  workflow_dispatch:
+
+
+env:
+  AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }}
+  AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }}
+  TOWER_ACCESS_TOKEN: ${{ secrets.AWS_TOWER_TOKEN }}
+  AWS_JOB_DEFINITION: ${{ secrets.AWS_JOB_DEFINITION }}
+  AWS_JOB_QUEUE: ${{ secrets.AWS_JOB_QUEUE }}
+  AWS_S3_BUCKET: ${{ secrets.AWS_S3_BUCKET }}
+
 
 jobs:
   run-awstest:
@@ -14,7 +23,7 @@ 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
@@ -23,17 +32,10 @@ jobs:
       - name: Start AWS batch job
         # For example: adding multiple test runs with different parameters
         # Remember that you can parallelise this by using strategy.matrix
-        env:
-          AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }}
-          AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }}
-          TOWER_ACCESS_TOKEN: ${{ secrets.AWS_TOWER_TOKEN }}
-          AWS_JOB_DEFINITION: ${{ secrets.AWS_JOB_DEFINITION }}
-          AWS_JOB_QUEUE: ${{ secrets.AWS_JOB_QUEUE }}
-          AWS_S3_BUCKET: ${{ secrets.AWS_S3_BUCKET }}
         run: |
           aws batch submit-job \
           --region eu-west-1 \
           --job-name nf-core-hic \
           --job-queue $AWS_JOB_QUEUE \
           --job-definition $AWS_JOB_DEFINITION \
-          --container-overrides '{"command": ["nf-core/hic", "-r '"${GITHUB_SHA}"' -profile test --outdir s3://'"${AWS_S3_BUCKET}"'/hic/results-'"${GITHUB_SHA}"' -w s3://'"${AWS_S3_BUCKET}"'/hic/work-'"${GITHUB_SHA}"' -with-tower"], "environment": [{"name": "TOWER_ACCESS_TOKEN", "value": "'"$TOWER_ACCESS_TOKEN"'"}]}'hic/work-'"${GITHUB_SHA}"' -with-tower"], "environment": [{"name": "TOWER_ACCESS_TOKEN", "value": "'"$TOWER_ACCESS_TOKEN"'"}]}'
+          --container-overrides '{"command": ["nf-core/hic", "-r '"${GITHUB_SHA}"' -profile test --outdir s3://'"${AWS_S3_BUCKET}"'/hic/results-'"${GITHUB_SHA}"' -w s3://'"${AWS_S3_BUCKET}"'/hic/work-'"${GITHUB_SHA}"' -with-tower"], "environment": [{"name": "TOWER_ACCESS_TOKEN", "value": "'"$TOWER_ACCESS_TOKEN"'"}]}'

.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:
@@ -13,7 +13,7 @@ jobs:
       - name: Check PRs
         if: github.repository == 'nf-core/hic'
         run: |
-          { [[ ${{github.event.pull_request.head.repo.full_name}} == nf-core/hic ]] && [[ $GITHUB_HEAD_REF = "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]]
+          { [[ ${{github.event.pull_request.head.repo.full_name }} == nf-core/hic ]] && [[ $GITHUB_HEAD_REF = "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]]
 
 
       # If the above check failed, post a comment on the PR explaining the failure
@@ -23,13 +23,22 @@ jobs:
         uses: mshick/add-pr-comment@v1
         with:
           message: |
+            ## This PR is against the `master` branch :x:
+
+            * Do not close this PR
+            * Click _Edit_ and change the `base` to `dev`
+            * This CI test will remain failed until you push a new commit
+
+            ---
+
             Hi @${{ github.event.pull_request.user.login }},
 
-            It looks like this pull-request is has been made against the ${{github.event.pull_request.head.repo.full_name}} `master` branch.
+            It looks like this pull-request is has been made against the [${{github.event.pull_request.head.repo.full_name }}](https://github.com/${{github.event.pull_request.head.repo.full_name }}) `master` branch.
             The `master` branch on nf-core repositories should always contain code from the latest release.
-            Because of this, PRs to `master` are only allowed if they come from the ${{github.event.pull_request.head.repo.full_name}} `dev` branch.
+            Because of this, PRs to `master` are only allowed if they come from the [${{github.event.pull_request.head.repo.full_name }}](https://github.com/${{github.event.pull_request.head.repo.full_name }}) `dev` branch.
 
             You do not need to close this PR, you can change the target branch to `dev` by clicking the _"Edit"_ button at the top of this page.
+            Note that even after this, the test will continue to show as failing until you push a new commit.
 
             Thanks again for your contribution!
           repo-token: ${{ secrets.GITHUB_TOKEN }}