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Template update for nf-core/tools version 2.0
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‎.editorconfig

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root = true
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[*]
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charset = utf-8
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end_of_line = lf
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insert_final_newline = true
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trim_trailing_whitespace = true
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indent_size = 4
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indent_style = space
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[*.{yml,yaml}]
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indent_size = 2
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# These files are edited and tested upstream in nf-core/modules
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[/modules/nf-core/**]
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charset = unset
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end_of_line = unset
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insert_final_newline = unset
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trim_trailing_whitespace = unset
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indent_style = unset
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indent_size = unset
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[/assets/email*]
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indent_size = unset

‎.github/CONTRIBUTING.md

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@@ -74,7 +74,7 @@ If you wish to contribute a new step, please use the following coding standards:
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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.yaml`.
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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`.

‎.github/ISSUE_TEMPLATE/bug_report.md

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I have checked the following places for your error:
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- [ ] [nf-core website: troubleshooting](https://nf-co.re/usage/troubleshooting)
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- [ ] [nf-core/rnaseq pipeline documentation](https://nf-co.re/nf-core/rnaseq/usage)
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- [ ] [nf-core/rnaseq pipeline documentation](https://nf-co.re/rnaseq/usage)
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## Description of the bug
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## Nextflow Installation
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- Version: <!-- [e.g. 19.10.0] -->
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- Version: <!-- [e.g. 21.04.0] -->
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## Container engine
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- Engine: <!-- [e.g. Conda, Docker, Singularity, Podman, Shifter or Charliecloud] -->
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- version: <!-- [e.g. 1.0.0] -->
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- Image tag: <!-- [e.g. nfcore/rnaseq:1.0.0] -->
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## Additional context
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‎.github/PULL_REQUEST_TEMPLATE.md

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- [ ] This comment contains a description of changes (with reason).
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- [ ] If you've fixed a bug or added code that should be tested, add tests!
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- [ ] If you've added a new tool - add to the software_versions process and a regex to `scrape_software_versions.py`
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- [ ] 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)
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- [ ] 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)
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- [ ] 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.
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- [ ] Make sure your code lints (`nf-core lint .`).
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- [ ] Ensure the test suite passes (`nextflow run . -profile test,docker`).

‎.github/workflows/awsfulltest.yml

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name: nf-core AWS full size tests
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# This workflow is triggered on published releases.
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# It can be additionally triggered manually with GitHub actions workflow dispatch.
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# It can be additionally triggered manually with GitHub actions workflow dispatch button.
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# It runs the -profile 'test_full' on AWS batch
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on:
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workflow_run:
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workflows: ["nf-core Docker push (release)"]
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types: [completed]
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release:
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types: [published]
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workflow_dispatch:
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env:
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AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }}
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AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }}
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TOWER_ACCESS_TOKEN: ${{ secrets.AWS_TOWER_TOKEN }}
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AWS_JOB_DEFINITION: ${{ secrets.AWS_JOB_DEFINITION }}
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AWS_JOB_QUEUE: ${{ secrets.AWS_JOB_QUEUE }}
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AWS_S3_BUCKET: ${{ secrets.AWS_S3_BUCKET }}
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jobs:
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run-awstest:
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run-tower:
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name: Run AWS full tests
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if: github.repository == 'nf-core/rnaseq'
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runs-on: ubuntu-latest
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steps:
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- name: Setup Miniconda
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uses: conda-incubator/setup-miniconda@v2
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with:
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auto-update-conda: true
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python-version: 3.7
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- name: Install awscli
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run: conda install -c conda-forge awscli
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- name: Start AWS batch job
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- name: Launch workflow via tower
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uses: nf-core/tower-action@master
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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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# Then specify `-profile test_full` instead of `-profile test` on the AWS batch command
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run: |
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aws batch submit-job \
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--region eu-west-1 \
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--job-name nf-core-rnaseq \
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--job-queue $AWS_JOB_QUEUE \
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--job-definition $AWS_JOB_DEFINITION \
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--container-overrides '{"command": ["nf-core/rnaseq", "-r '"${GITHUB_SHA}"' -profile test --outdir s3://'"${AWS_S3_BUCKET}"'/rnaseq/results-'"${GITHUB_SHA}"' -w s3://'"${AWS_S3_BUCKET}"'/rnaseq/work-'"${GITHUB_SHA}"' -with-tower"], "environment": [{"name": "TOWER_ACCESS_TOKEN", "value": "'"$TOWER_ACCESS_TOKEN"'"}]}'
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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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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/rnaseq/work-${{ github.sha }}
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parameters: |
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{
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"outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/rnaseq/results-${{ github.sha }}"
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}
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profiles: '[ "test_full", "aws_tower" ]'
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‎.github/workflows/awstest.yml

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name: nf-core AWS test
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# This workflow is triggered on push to the master branch.
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# It can be additionally triggered manually with GitHub actions workflow dispatch.
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# It runs the -profile 'test' on AWS batch.
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# This workflow can be triggered manually with the GitHub actions workflow dispatch button.
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# It runs the -profile 'test' on AWS batch
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on:
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workflow_dispatch:
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env:
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AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }}
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AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }}
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TOWER_ACCESS_TOKEN: ${{ secrets.AWS_TOWER_TOKEN }}
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AWS_JOB_DEFINITION: ${{ secrets.AWS_JOB_DEFINITION }}
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AWS_JOB_QUEUE: ${{ secrets.AWS_JOB_QUEUE }}
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AWS_S3_BUCKET: ${{ secrets.AWS_S3_BUCKET }}
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jobs:
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run-awstest:
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run-tower:
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name: Run AWS tests
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if: github.repository == 'nf-core/rnaseq'
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runs-on: ubuntu-latest
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steps:
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- name: Setup Miniconda
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uses: conda-incubator/setup-miniconda@v2
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- name: Launch workflow via tower
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uses: nf-core/tower-action@master
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with:
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auto-update-conda: true
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python-version: 3.7
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- name: Install awscli
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run: conda install -c conda-forge awscli
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- name: Start AWS batch job
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# TODO nf-core: You can customise CI pipeline run tests as required
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# For example: adding multiple test runs with different parameters
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# Remember that you can parallelise this by using strategy.matrix
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run: |
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aws batch submit-job \
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--region eu-west-1 \
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--job-name nf-core-rnaseq \
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--job-queue $AWS_JOB_QUEUE \
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--job-definition $AWS_JOB_DEFINITION \
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--container-overrides '{"command": ["nf-core/rnaseq", "-r '"${GITHUB_SHA}"' -profile test --outdir s3://'"${AWS_S3_BUCKET}"'/rnaseq/results-'"${GITHUB_SHA}"' -w s3://'"${AWS_S3_BUCKET}"'/rnaseq/work-'"${GITHUB_SHA}"' -with-tower"], "environment": [{"name": "TOWER_ACCESS_TOKEN", "value": "'"$TOWER_ACCESS_TOKEN"'"}]}'
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workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
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bearer_token: ${{ secrets.TOWER_BEARER_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/rnaseq/work-${{ github.sha }}
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parameters: |
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{
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"outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/rnaseq/results-${{ github.sha }}"
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}
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profiles: '[ "test", "aws_tower" ]'
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‎.github/workflows/ci.yml

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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: ['20.04.0', '']
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nxf_ver: ['21.04.0', '']
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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: Check if Dockerfile or Conda environment changed
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uses: technote-space/get-diff-action@v4
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with:
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FILES: |
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Dockerfile
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environment.yml
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- name: Build new docker image
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if: env.MATCHED_FILES
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run: docker build --no-cache . -t nfcore/rnaseq:dev
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- name: Pull docker image
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if: ${{ !env.MATCHED_FILES }}
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run: |
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docker pull nfcore/rnaseq:dev
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docker tag nfcore/rnaseq:dev nfcore/rnaseq:dev
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- name: Install Nextflow
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env:
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CAPSULE_LOG: none

‎.github/workflows/linting.yml

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- name: Install markdownlint
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run: npm install -g markdownlint-cli
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- name: Run Markdownlint
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run: markdownlint ${GITHUB_WORKSPACE} -c ${GITHUB_WORKSPACE}/.github/markdownlint.yml
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run: markdownlint .
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# If the above check failed, post a comment on the PR explaining the failure
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- name: Post PR comment
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* On Mac: `brew install markdownlint-cli`
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* Everything else: [Install `npm`](https://www.npmjs.com/get-npm) then [install `markdownlint-cli`](https://www.npmjs.com/package/markdownlint-cli) (`npm install -g markdownlint-cli`)
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* Fix the markdown errors
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* Automatically: `markdownlint . --config .github/markdownlint.yml --fix`
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* Manually resolve anything left from `markdownlint . --config .github/markdownlint.yml`
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* Automatically: `markdownlint . --fix`
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* Manually resolve anything left from `markdownlint .`
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Once you push these changes the test should pass, and you can hide this comment :+1:
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repo-token: ${{ secrets.GITHUB_TOKEN }}
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allow-repeats: false
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EditorConfig:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v2
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- uses: actions/setup-node@v1
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with:
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node-version: "10"
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- name: Install editorconfig-checker
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run: npm install -g editorconfig-checker
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- name: Run ECLint check
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run: editorconfig-checker -exclude README.md $(git ls-files | grep -v test)
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YAML:
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nf-core:
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runs-on: ubuntu-latest
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steps:

‎.github/workflows/push_dockerhub_dev.yml

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‎.github/workflows/push_dockerhub_release.yml

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‎.gitignore

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data/
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results/
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.DS_Store
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tests/
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testing/
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testing*
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*.pyc

‎.github/markdownlint.yml ‎.markdownlint.yml

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# Markdownlint configuration file
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default: true
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line-length: false
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ul-indent:
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indent: 4
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no-duplicate-header:
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siblings_only: true
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no-inline-html:

‎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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## v3.3dev - [date]
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Initial release of nf-core/rnaseq, created with the [nf-core](https://nf-co.re/) template.
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‎CITATIONS.md

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# nf-core/rnaseq: Citations
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## [nf-core](https://pubmed.ncbi.nlm.nih.gov/32055031/)
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> Ewels PA, Peltzer A, Fillinger S, Patel H, Alneberg J, Wilm A, Garcia MU, Di Tommaso P, Nahnsen S. The nf-core framework for community-curated bioinformatics pipelines. Nat Biotechnol. 2020 Mar;38(3):276-278. doi: 10.1038/s41587-020-0439-x. PubMed PMID: 32055031.
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## [Nextflow](https://pubmed.ncbi.nlm.nih.gov/28398311/)
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> Di Tommaso P, Chatzou M, Floden EW, Barja PP, Palumbo E, Notredame C. Nextflow enables reproducible computational workflows. Nat Biotechnol. 2017 Apr 11;35(4):316-319. doi: 10.1038/nbt.3820. PubMed PMID: 28398311.
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## Pipeline tools
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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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> 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
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* [Anaconda](https://anaconda.com)
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> Anaconda Software Distribution. Computer software. Vers. 2-2.4.0. Anaconda, Nov. 2016. Web.
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* [Bioconda](https://pubmed.ncbi.nlm.nih.gov/29967506/)
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> Grüning B, Dale R, Sjödin A, Chapman BA, Rowe J, Tomkins-Tinch CH, Valieris R, Köster J; Bioconda Team. Bioconda: sustainable and comprehensive software distribution for the life sciences. Nat Methods. 2018 Jul;15(7):475-476. doi: 10.1038/s41592-018-0046-7. PubMed PMID: 29967506.
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* [BioContainers](https://pubmed.ncbi.nlm.nih.gov/28379341/)
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> da Veiga Leprevost F, Grüning B, Aflitos SA, Röst HL, Uszkoreit J, Barsnes H, Vaudel M, Moreno P, Gatto L, Weber J, Bai M, Jimenez RC, Sachsenberg T, Pfeuffer J, Alvarez RV, Griss J, Nesvizhskii AI, Perez-Riverol Y. BioContainers: an open-source and community-driven framework for software standardization. Bioinformatics. 2017 Aug 15;33(16):2580-2582. doi: 10.1093/bioinformatics/btx192. PubMed PMID: 28379341; PubMed Central PMCID: PMC5870671.
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* [Docker](https://dl.acm.org/doi/10.5555/2600239.2600241)
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* [Singularity](https://pubmed.ncbi.nlm.nih.gov/28494014/)
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> Kurtzer GM, Sochat V, Bauer MW. Singularity: Scientific containers for mobility of compute. PLoS One. 2017 May 11;12(5):e0177459. doi: 10.1371/journal.pone.0177459. eCollection 2017. PubMed PMID: 28494014; PubMed Central PMCID: PMC5426675.

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