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Merge pull request #49 from nf-core/dev
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‎.github/ISSUE_TEMPLATE/bug_report.md‎

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---
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name: Bug report
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about: Create a report to help us improve
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title: ''
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labels: ''
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assignees: ''
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---
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# nf-core/eager bug report
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Hi there!
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Thanks for telling us about a problem with the pipeline.
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Please delete this text and anything that's not relevant from the template below:
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## Check Documentation
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Have you checked in the following places for your error?:
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- [ ] [Frequently Asked Questions](https://nf-co.re/eager/docs/faq)
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(for nf-core/eager specific information)
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- [ ] [Troubleshooting](https://nf-co.re/usage/troubleshooting)
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(for nf-core specific information)
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Please also check the the corresponding branch documentation on github, if not
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testing the latest release.
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## Describe the bug
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A clear and concise description of what you expected to happen.
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## Log files
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1. The command use to run the pipeline
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2. The `.nextflow.log` file (which a hidden file in which ever place you _ran_
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the pipeline from - not necessarily the output directory!)
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## System
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- Hardware: <!-- [e.g. HPC, Desktop, Cloud...] -->

‎.github/ISSUE_TEMPLATE/feature_request.md‎

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---
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name: Feature request
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about: Suggest an idea for this project
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title: ''
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labels: ''
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assignees: ''
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---
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# nf-core/eager feature request
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Hi there!
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Thanks for suggesting a new feature for the pipeline!
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Please delete this text and anything that's not relevant from the template below:
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## Is your feature request related to a problem? Please describe
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‎.github/markdownlint.yml‎

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allowed_elements:
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- img
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- p
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- kbd

‎.github/workflows/awsfulltest.yml‎

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name: nf-core AWS full test
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# This workflow is triggered on push to the master branch and on published releases.
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# It runs the -profile 'test_full' on AWS batch
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on:
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release:
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types: [published]
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jobs:
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run-awstest:
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if: github.repository == 'nf-core/eager'
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name: Run AWS full tests
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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: goanpeca/setup-miniconda@v1.0.2
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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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# 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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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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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-eager \
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--job-queue $AWS_JOB_QUEUE \
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--job-definition $AWS_JOB_DEFINITION \
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--container-overrides '{"command": ["nf-core/eager", "-r '"${GITHUB_SHA}"' -profile test_full --outdir s3://'"${AWS_S3_BUCKET}"'/eager/results-'"${GITHUB_SHA}"' -w s3://'"${AWS_S3_BUCKET}"'/eager/work-'"${GITHUB_SHA}"' -with-tower"], "environment": [{"name": "TOWER_ACCESS_TOKEN", "value": "'"$TOWER_ACCESS_TOKEN"'"}]}'

‎.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 and on published releases.
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# It runs the -profile 'test_tsv' on AWS batch
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on:
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push:
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branches:
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- master
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jobs:
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run-awstest:
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if: github.repository == 'nf-core/eager'
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name: Run AWS test
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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: goanpeca/setup-miniconda@v1.0.2
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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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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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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-eager \
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--job-queue $AWS_JOB_QUEUE \
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--job-definition $AWS_JOB_DEFINITION \
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--container-overrides '{"command": ["nf-core/eager", "-r '"${GITHUB_SHA}"' -profile test_tsv --outdir s3://'"${AWS_S3_BUCKET}"'/eager/results-'"${GITHUB_SHA}"' -w s3://'"${AWS_S3_BUCKET}"'/eager/work-'"${GITHUB_SHA}"' -with-tower"], "environment": [{"name": "TOWER_ACCESS_TOKEN", "value": "'"$TOWER_ACCESS_TOKEN"'"}]}'

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