Important! Template update for nf-core/tools v1.10.2

[nf-core-bot]

A new release of the main template in nf-core/tools has just been released. This automated pull-request attempts to apply the relevant updates to this pipeline.

Please make sure to merge this pull-request as soon as possible. Once complete, make a new minor release of your pipeline. For instructions on how to merge this PR, please see https://nf-co.re/developers/sync.

For more information about this release of nf-core/tools, please see the nf-core/tools v1.10.2 release page.

[github-actions]

nf-core lint overall result: Passed ✅

Updated for pipeline commit 1d86be2

+| ✅ 85 tests passed       |+
!| ❗ 32 tests had warnings |!
-| ❌  0 tests failed       |-

❗ Test warnings:

• Test #5 - GitHub Actions AWS full test should test full datasets: /home/runner/work/gwas/gwas/.github/workflows/awsfulltest.yml
• Test #8 - Conda package is not latest available: conda-forge::python=3.7.3, 3.8.5 available
• Test #8 - Conda package is not latest available: conda-forge::markdown=3.1.1, 3.2.2 available
• Test #8 - Conda package is not latest available: conda-forge::pymdown-extensions=6.0, 7.1 available
• Test #8 - Conda package is not latest available: conda-forge::pygments=2.5.2, 2.6.1 available
• Test #8 - Conda package is not latest available: bioconda::fastqc=0.11.8, 0.11.9 available
• Test #8 - Conda package is not latest available: bioconda::multiqc=1.7, 1.9 available
• Test #10 - TODO string found in main.nf: Add to this help message with new command line parameters
• Test #10 - TODO string found in main.nf: Add any reference files that are needed
• Test #10 - TODO string found in main.nf: Report custom parameters here
• Test #10 - TODO string found in main.nf: Get all tools to print their version number here
• Test #10 - TODO string found in main.nf: Add in log files from your new processes for MultiQC to find!
• Test #10 - TODO string found in main.nf: Specify which MultiQC modules to use with -m for a faster run time
• Test #10 - TODO string found in main.nf: If not using MultiQC, strip out this code (including params.max_multiqc_email_size)
• Test #10 - TODO string found in nextflow.config: Specify your pipeline's command line flags
• Test #10 - TODO string found in README.md: Update the example "typical command" below used to run the pipeline
• Test #10 - TODO string found in README.md: Add a brief overview of what the pipeline does and how it works
• Test #10 - TODO string found in README.md: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi.
• Test #10 - TODO string found in environment.yml: Add required software dependencies here
• Test #10 - TODO string found in test.config: Specify the paths to your test data on nf-core/test-datasets
• Test #10 - TODO string found in test.config: Give any required params for the test so that command line flags are not needed
• Test #10 - TODO string found in test_full.config: Specify the paths to your full test data ( on nf-core/test-datasets or directly in repositories, e.g. SRA)
• Test #10 - TODO string found in test_full.config: Give any required params for the test so that command line flags are not needed
• Test #10 - TODO string found in base.config: Check the defaults for all processes
• Test #10 - TODO string found in base.config: Customise requirements for specific processes.
• Test #10 - TODO string found in ci.yml: You can customise CI pipeline run tests as required
• Test #10 - TODO string found in awstest.yml: You can customise CI pipeline run tests as required
• Test #10 - TODO string found in awsfulltest.yml: You can customise AWS full pipeline tests as required
• Test #10 - TODO string found in scrape_software_versions.py: Add additional regexes for new tools in process get_software_versions
• Test #10 - TODO string found in usage.md: Add documentation about anything specific to running your pipeline. For general topics, please point to (and add to) the main nf-core website.
• Test #10 - TODO string found in README.md: If you write more documentation pages, add them to the docs index page here
• Test #10 - TODO string found in output.md: Write this documentation describing your workflow's output

✅ Tests passed:

• Test #1 - File found: nextflow.config
• Test #1 - File found: nextflow_schema.json
• Test #1 - File found: Dockerfile
• 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: 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: .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/gwas:dev
• Test #4 - Config manifest.version ends in dev: '1.0dev'
• Test #5 - GitHub Actions 'branch' workflow is triggered for PRs to master: /home/runner/work/gwas/gwas/.github/workflows/branch.yml
• Test #5 - GitHub Actions 'branch' workflow looks good: /home/runner/work/gwas/gwas/.github/workflows/branch.yml
• Test #5 - GitHub Actions CI is triggered on expected events: /home/runner/work/gwas/gwas/.github/workflows/ci.yml
• Test #5 - CI is building the correct docker image: docker build --no-cache . -t nfcore/gwas:dev
• Test #5 - CI is pulling the correct docker image: docker pull nfcore/gwas:dev
• Test #5 - CI is tagging docker image correctly: docker tag nfcore/gwas:dev nfcore/gwas:dev
• Test #5 - Continuous integration checks minimum NF version: /home/runner/work/gwas/gwas/.github/workflows/ci.yml
• Test #5 - GitHub Actions linting workflow is triggered on PR and push: /home/runner/work/gwas/gwas/.github/workflows/linting.yml
• Test #5 - Continuous integration runs Markdown lint Tests: /home/runner/work/gwas/gwas/.github/workflows/linting.yml
• Test #5 - Continuous integration runs nf-core lint Tests: /home/runner/work/gwas/gwas/.github/workflows/linting.yml
• Test #5 - GitHub Actions AWS test is triggered on push and not PRs: /home/runner/work/gwas/gwas/.github/workflows/awstest.yml
• Test #5 - GitHub Actions AWS test is triggered only on push to master: /home/runner/work/gwas/gwas/.github/workflows/awstest.yml
• Test #5 - GitHub Actions AWS full test is triggered only on published release: /home/runner/work/gwas/gwas/.github/workflows/awsfulltest.yml
• Test #6 - README Nextflow minimum version badge matched config. Badge: 19.10.0, Config: 19.10.0
• Test #6 - README had a bioconda badge
• Test #8 - Conda environment name was correct (nf-core-gwas-1.0dev)
• Test #8 - Conda dependency had pinned version number: conda-forge::python=3.7.3
• Test #8 - Conda dependency had pinned version number: conda-forge::markdown=3.1.1
• Test #8 - Conda dependency had pinned version number: conda-forge::pymdown-extensions=6.0
• Test #8 - Conda dependency had pinned version number: conda-forge::pygments=2.5.2
• Test #8 - Conda dependency had pinned version number: bioconda::fastqc=0.11.8
• Test #8 - Conda dependency had pinned version number: bioconda::multiqc=1.7
• Test #9 - Found all expected strings in Dockerfile file
• Test #12 - Name adheres to nf-core convention
• Test #13 - Did not find any cookiecutter template strings (38 files)
• Test #14 - Schema lint passed
• Test #14 - Schema title + description lint passed
• Test #15 - Schema matched params returned from nextflow config

Run details:

• nf-core/tools version 1.10.2
• Run at 2020-07-31 11:22:44

[pappewaio]

The test is not yet in place, although the test data exists and just need to be linked to from the main.nf script.
So I will merge this pull request.