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Template update for nf-core/tools version 2.2
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‎.gitattributes

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*.config linguist-language=nextflow
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modules/nf-core/** linguist-generated
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subworkflows/nf-core/** linguist-generated

‎.github/CONTRIBUTING.md

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1. Define the corresponding input channel into your new process from the expected previous process channel
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2. Write the process block (see below).
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3. Define the output channel if needed (see below).
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4. Add any new flags/options to `nextflow.config` with a default (see below).
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5. Add any new flags/options to `nextflow_schema.json` with help text (with `nf-core schema build`).
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6. Add any new flags/options to the help message (for integer/text parameters, print to help the corresponding `nextflow.config` parameter).
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7. Add sanity checks for all relevant parameters.
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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`.
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9. Do local tests that the new code works properly and as expected.
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10. Add a new test command in `.github/workflow/ci.yml`.
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11. If applicable add a [MultiQC](https://https://multiqc.info/) module.
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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.
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13. Optional: Add any descriptions of MultiQC report sections and output files to `docs/output.md`.
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4. Add any new parameters to `nextflow.config` with a default (see below).
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5. Add any new parameters to `nextflow_schema.json` with help text (via the `nf-core schema build` tool).
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6. Add sanity checks and validation for all relevant parameters.
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7. Perform local tests to validate that the new code works as expected.
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8. If applicable, add a new test command in `.github/workflow/ci.yml`.
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9. Update MultiQC config `assets/multiqc_config.yaml` so relevant suffixes, file name clean up and module plots are in the appropriate order. If applicable, add a [MultiQC](https://https://multiqc.info/) module.
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10. Add a description of the output files and if relevant any appropriate images from the MultiQC report to `docs/output.md`.
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### Default values
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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]`
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### Software version reporting
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If you add a new tool to the pipeline, please ensure you add the information of the tool to the `get_software_version` process.
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Add to the script block of the process, something like the following:
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```bash
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<YOUR_TOOL> --version &> v_<YOUR_TOOL>.txt 2>&1 || true
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```
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or
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```bash
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<YOUR_TOOL> --help | head -n 1 &> v_<YOUR_TOOL>.txt 2>&1 || true
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```
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You then need to edit the script `bin/scrape_software_versions.py` to:
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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`
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2. Add a HTML entry to the `OrderedDict` for formatting in MultiQC.
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### Images and figures
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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

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‎.github/ISSUE_TEMPLATE/bug_report.yml

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name: Bug report
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description: Report something that is broken or incorrect
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labels: bug
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body:
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- type: markdown
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attributes:
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value: |
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Before you post this issue, please check the documentation:
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- [nf-core website: troubleshooting](https://nf-co.re/usage/troubleshooting)
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- [nf-core/rnavar pipeline documentation](https://nf-co.re/rnavar/usage)
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- type: textarea
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id: description
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attributes:
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label: Description of the bug
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description: A clear and concise description of what the bug is.
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validations:
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required: true
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- type: textarea
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id: command_used
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attributes:
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label: Command used and terminal output
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description: Steps to reproduce the behaviour. Please paste the command you used to launch the pipeline and the output from your terminal.
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render: console
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placeholder: |
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$ nextflow run ...
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Some output where something broke
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- type: textarea
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id: files
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attributes:
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label: Relevant files
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description: |
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Please drag and drop the relevant files here. Create a `.zip` archive if the extension is not allowed.
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Your verbose log file `.nextflow.log` is often useful _(this is a hidden file in the directory where you launched the pipeline)_ as well as custom Nextflow configuration files.
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- type: textarea
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id: system
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attributes:
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label: System information
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description: |
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* Nextflow version _(eg. 21.10.3)_
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* Hardware _(eg. HPC, Desktop, Cloud)_
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* Executor _(eg. slurm, local, awsbatch)_
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* Container engine: _(e.g. Docker, Singularity, Conda, Podman, Shifter or Charliecloud)_
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* OS _(eg. CentOS Linux, macOS, Linux Mint)_
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* Version of nf-core/rnavar _(eg. 1.1, 1.5, 1.8.2)_

‎.github/ISSUE_TEMPLATE/config.yml

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blank_issues_enabled: false
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contact_links:
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- name: Join nf-core
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url: https://nf-co.re/join

‎.github/ISSUE_TEMPLATE/feature_request.md

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‎.github/ISSUE_TEMPLATE/feature_request.yml

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name: Feature request
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description: Suggest an idea for the nf-core/rnavar pipeline
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labels: enhancement
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body:
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- type: textarea
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id: description
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attributes:
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label: Description of feature
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description: Please describe your suggestion for a new feature. It might help to describe a problem or use case, plus any alternatives that you have considered.
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validations:
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required: true

‎.github/workflows/awsfulltest.yml

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runs-on: ubuntu-latest
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steps:
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- name: Launch workflow via tower
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uses: nf-core/tower-action@master
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uses: nf-core/tower-action@v2
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# TODO nf-core: You can customise AWS full pipeline tests as required
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# Add full size test data (but still relatively small datasets for few samples)
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# on the `test_full.config` test runs with only one set of parameters
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with:
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workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
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bearer_token: ${{ secrets.TOWER_BEARER_TOKEN }}
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access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
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compute_env: ${{ secrets.TOWER_COMPUTE_ENV }}
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pipeline: ${{ github.repository }}
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revision: ${{ github.sha }}
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{
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"outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/rnavar/results-${{ github.sha }}"
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}
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profiles: '[ "test_full", "aws_tower" ]'
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profiles: test_full,aws_tower
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pre_run_script: 'export NXF_VER=21.10.3'

‎.github/workflows/awstest.yml

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runs-on: ubuntu-latest
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steps:
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- name: Launch workflow via tower
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uses: nf-core/tower-action@master
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uses: nf-core/tower-action@v2
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with:
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workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
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bearer_token: ${{ secrets.TOWER_BEARER_TOKEN }}
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access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
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compute_env: ${{ secrets.TOWER_COMPUTE_ENV }}
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pipeline: ${{ github.repository }}
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revision: ${{ github.sha }}
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workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/rnavar/work-${{ github.sha }}
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parameters: |
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{
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"outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/rnavar/results-${{ github.sha }}"
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"outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/rnavar/results-test-${{ github.sha }}"
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}
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profiles: '[ "test", "aws_tower" ]'
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profiles: test,aws_tower
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pre_run_script: 'export NXF_VER=21.10.3'

‎.github/workflows/ci.yml

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release:
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types: [published]
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# Uncomment if we need an edge release of Nextflow again
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# env: NXF_EDGE: 1
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env:
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NXF_ANSI_LOG: false
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CAPSULE_LOG: none
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jobs:
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test:
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name: Run workflow tests
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# Only run on push if this is the nf-core dev branch (merged PRs)
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if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/rnavar') }}
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runs-on: ubuntu-latest
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env:
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NXF_VER: ${{ matrix.nxf_ver }}
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NXF_ANSI_LOG: false
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strategy:
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matrix:
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# Nextflow versions: check pipeline minimum and current latest
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nxf_ver: ['21.04.0', '']
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# Nextflow versions
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include:
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# Test pipeline minimum Nextflow version
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- NXF_VER: '21.10.3'
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NXF_EDGE: ''
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# Test latest edge release of Nextflow
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- NXF_VER: ''
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NXF_EDGE: '1'
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steps:
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- name: Check out pipeline code
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uses: actions/checkout@v2
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- name: Install Nextflow
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env:
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CAPSULE_LOG: none
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NXF_VER: ${{ matrix.NXF_VER }}
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# Uncomment only if the edge release is more recent than the latest stable release
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# See https://github.com/nextflow-io/nextflow/issues/2467
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# NXF_EDGE: ${{ matrix.NXF_EDGE }}
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run: |
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wget -qO- get.nextflow.io | bash
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sudo mv nextflow /usr/local/bin/

‎.github/workflows/linting_comment.yml

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uses: dawidd6/action-download-artifact@v2
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with:
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workflow: linting.yml
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workflow_conclusion: completed
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- name: Get PR number
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id: pr_number

‎CHANGELOG.md

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The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
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and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
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## v3.1 - [date]
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## v1.0dev - [date]
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Initial release of nf-core/rnavar, created with the [nf-core](https://nf-co.re/) template.
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‎CITATIONS.md

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* [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
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* [MultiQC](https://www.ncbi.nlm.nih.gov/pubmed/27312411/)
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* [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/)
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> Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924.
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## Software packaging/containerisation tools

‎LICENSE

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MIT License
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Copyright (c) Praveen Raj
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Copyright (c) @praveenraj2018
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Permission is hereby granted, free of charge, to any person obtaining a copy
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of this software and associated documentation files (the "Software"), to deal

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