Update environment.yml

[maxulysse]

Update control-freec

nf-core/sarek pull request

Many thanks for contributing to nf-core/sarek!

Please fill in the appropriate checklist below (delete whatever is not relevant).
These are the most common things requested on pull requests (PRs).

PR checklist

• This comment contains a description of changes (with reason)
• If you've fixed a bug or added code that should be tested, add tests!
• If necessary, also make a PR on the nf-core/sarek branch on the nf-core/test-datasets repo
• Ensure the test suite passes (nextflow run . -profile test,docker).
• Make sure your code lints (nf-core lint .).
• Documentation in docs is updated
• CHANGELOG.md is updated
• README.md is updated

Learn more about contributing: CONTRIBUTING.md

[github-actions]

nf-core lint overall result: Failed ❌

Posted for pipeline commit d662de2

+| ✅ 68 tests passed       |+
!| ❗  0 tests had warnings |!
-| ❌  1 tests failed       |-

❌ Test failures:

• Test #5 - GitHub Actions AWS test should be triggered on workflow_dispatch and not on push or PRs: /home/runner/work/sarek/sarek/.github/workflows/awstest.yml

✅ Tests passed:

• Test #1 - File found: nextflow.config
• Test #1 - File found: nextflow_schema.json
• Test #1 - File found: LICENSE or LICENSE.md or LICENCE or LICENCE.md
• Test #1 - File found: README.md
• Test #1 - File found: CHANGELOG.md
• Test #1 - File found: docs/README.md
• Test #1 - File found: docs/output.md
• Test #1 - File found: docs/usage.md
• Test #1 - File found: .github/workflows/branch.yml
• Test #1 - File found: .github/workflows/ci.yml
• Test #1 - File found: .github/workflows/linting.yml
• Test #1 - File found: main.nf
• Test #1 - File found: environment.yml
• Test #1 - File found: Dockerfile
• Test #1 - File found: conf/base.config
• Test #1 - File found: .github/workflows/awstest.yml
• Test #1 - File found: .github/workflows/awsfulltest.yml
• Test #1 - File not found check: Singularity
• Test #1 - File not found check: parameters.settings.json
• Test #1 - File not found check: bin/markdown_to_html.r
• Test #1 - File not found check: .travis.yml
• Test #3 - Licence check passed
• Test #2 - Dockerfile check passed
• Test #4 - Config variable found: manifest.name
• Test #4 - Config variable found: manifest.nextflowVersion
• Test #4 - Config variable found: manifest.description
• Test #4 - Config variable found: manifest.version
• Test #4 - Config variable found: manifest.homePage
• Test #4 - Config variable found: timeline.enabled
• Test #4 - Config variable found: trace.enabled
• Test #4 - Config variable found: report.enabled
• Test #4 - Config variable found: dag.enabled
• Test #4 - Config variable found: process.cpus
• Test #4 - Config variable found: process.memory
• Test #4 - Config variable found: process.time
• Test #4 - Config variable found: params.outdir
• Test #4 - Config variable found: params.input
• Test #4 - Config variable found: manifest.mainScript
• Test #4 - Config variable found: timeline.file
• Test #4 - Config variable found: trace.file
• Test #4 - Config variable found: report.file
• Test #4 - Config variable found: dag.file
• Test #4 - Config variable found: process.container
• Test #4 - Config variable (correctly) not found: params.version
• Test #4 - Config variable (correctly) not found: params.nf_required_version
• Test #4 - Config variable (correctly) not found: params.container
• Test #4 - Config variable (correctly) not found: params.singleEnd
• Test #4 - Config variable (correctly) not found: params.igenomesIgnore
• Test #4 - Config timeline.enabled had correct value: true
• Test #4 - Config report.enabled had correct value: true
• Test #4 - Config trace.enabled had correct value: true
• Test #4 - Config dag.enabled had correct value: true
• Test #4 - Config manifest.name began with nf-core/
• Test #4 - Config variable manifest.homePage began with https://github.com/nf-core/
• Test #4 - Config dag.file ended with .svg
• Test #4 - Config variable manifest.nextflowVersion started with >= or !>=
• Test #4 - Config process.container looks correct: nfcore/sarek:dev
• Test #4 - Config manifest.version ends in dev: '3.0dev'
• Test #5 - GitHub Actions 'branch' workflow is triggered for PRs to master: /home/runner/work/sarek/sarek/.github/workflows/branch.yml
• Test #5 - GitHub Actions 'branch' workflow looks good: /home/runner/work/sarek/sarek/.github/workflows/branch.yml
• Test #5 - GitHub Actions CI is triggered on expected events: /home/runner/work/sarek/sarek/.github/workflows/ci.yml
• Test #5 - CI is building the correct docker image: docker build --no-cache . -t nfcore/sarek:dev
• Test #5 - CI is pulling the correct docker image: docker pull nfcore/sarek:dev
• Test #5 - CI is tagging docker image correctly: docker tag nfcore/sarek:dev nfcore/sarek:dev
• Test #5 - Continuous integration checks minimum NF version: /home/runner/work/sarek/sarek/.github/workflows/ci.yml
• Test #5 - GitHub Actions linting workflow is triggered on PR and push: /home/runner/work/sarek/sarek/.github/workflows/linting.yml
• Test #5 - Continuous integration runs Markdown lint Tests: /home/runner/work/sarek/sarek/.github/workflows/linting.yml
• Test #5 - Continuous integration runs nf-core lint Tests: /home/runner/work/sarek/sarek/.github/workflows/linting.yml

Run details:

• nf-core/tools version 1.11
• Run at 2020-11-17 12:01:37

[maxulysse]

cf #302