Example tutorials

[jfy133]

nf-core/eager pull request

This PR contains example tutorials on how to set up EAGER runs for different contexts.

Tutorials should include:

• Preparation (what extra files you need, and examples where you can get them from)
• Walkthrough of which parameters are set with short explanations/justifications
• Brief description of MultiQC report (and how to evalute), and where to find most important output files.

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/eager branch on the nf-core/test-datasets repo
• Ensure the test suite passes (nextflow run . -profile test,docker --paired_end).
• 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

[jfy133]

@TCLamnidis

[jfy133]

You still have some unresolved suggestions, but the outlier thing is good and I tweaked the SNP desciption.

[github-actions]

nf-core lint overall result: Passed ✅

Posted for pipeline commit ec4cb46

+| ✅ 149 tests passed       |+
!| ❗ 10 tests had warnings |!
-| ❌  0 tests failed       |-

❗ Test warnings:

• 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::openjdk=8.0.144, 11.0.8 available
• Test #8 - Conda package is not latest available: bioconda::picard=2.22.9, 2.23.3 available
• Test #8 - Conda package is not latest available: bioconda::samtools=1.9, 1.10 available
• Test #8 - Conda package is not latest available: bioconda::gatk4=4.1.7.0, 4.1.8.1 available
• Test #8 - Conda package is not latest available: pysam=0.15.4, 0.16.0.1 available
• Test #8 - Conda package is not latest available: conda-forge::pandas=1.0.4, 1.1.0 available
• Test #8 - Conda package is not latest available: conda-forge::biopython=1.76, 1.77 available
• Test #15 - Schema param awsqueue not found from nextflow config
• Test #15 - Schema param awsregion not found from nextflow config

✅ 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/eager:dev
• Test #4 - Config manifest.version ends in dev: '2.2.0dev'
• Test #5 - GitHub Actions 'branch' workflow is triggered for PRs to master: /home/runner/work/eager/eager/.github/workflows/branch.yml
• Test #5 - GitHub Actions 'branch' workflow looks good: /home/runner/work/eager/eager/.github/workflows/branch.yml
• Test #5 - GitHub Actions CI is triggered on expected events: /home/runner/work/eager/eager/.github/workflows/ci.yml
• Test #5 - CI is building the correct docker image: docker build --no-cache . -t nfcore/eager:dev
• Test #5 - CI is pulling the correct docker image: docker pull nfcore/eager:dev
• Test #5 - CI is tagging docker image correctly: docker tag nfcore/eager:dev nfcore/eager:dev
• Test #5 - Continuous integration checks minimum NF version: /home/runner/work/eager/eager/.github/workflows/ci.yml
• Test #5 - GitHub Actions linting workflow is triggered on PR and push: /home/runner/work/eager/eager/.github/workflows/linting.yml
• Test #5 - Continuous integration runs Markdown lint Tests: /home/runner/work/eager/eager/.github/workflows/linting.yml
• Test #5 - Continuous integration runs nf-core lint Tests: /home/runner/work/eager/eager/.github/workflows/linting.yml
• Test #5 - GitHub Actions AWS test is triggered on push and not PRs: /home/runner/work/eager/eager/.github/workflows/awstest.yml
• Test #5 - GitHub Actions AWS test is triggered only on push to master: /home/runner/work/eager/eager/.github/workflows/awstest.yml
• Test #5 - GitHub Actions AWS full test is triggered only on published release: /home/runner/work/eager/eager/.github/workflows/awsfulltest.yml
• Test #5 - GitHub Actions AWS full test should test full datasets: /home/runner/work/eager/eager/.github/workflows/awsfulltest.yml
• Test #6 - README Nextflow minimum version badge matched config. Badge: 20.04.0, Config: 20.04.0
• Test #6 - README had a bioconda badge
• Test #8 - Conda environment name was correct (nf-core-eager-2.2.0dev)
• 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=3.2.2
• Test #8 - Conda package is latest available: conda-forge::markdown=3.2.2
• Test #8 - Conda dependency had pinned version number: conda-forge::pymdown-extensions=7.1
• Test #8 - Conda package is latest available: conda-forge::pymdown-extensions=7.1
• Test #8 - Conda dependency had pinned version number: conda-forge::pygments=2.6.1
• Test #8 - Conda package is latest available: conda-forge::pygments=2.6.1
• Test #8 - Conda dependency had pinned version number: bioconda::rename=1.601
• Test #8 - Conda package is latest available: bioconda::rename=1.601
• Test #8 - Conda dependency had pinned version number: conda-forge::openjdk=8.0.144
• Test #8 - Conda dependency had pinned version number: bioconda::fastqc=0.11.9
• Test #8 - Conda package is latest available: bioconda::fastqc=0.11.9
• Test #8 - Conda dependency had pinned version number: bioconda::adapterremoval=2.3.1
• Test #8 - Conda package is latest available: bioconda::adapterremoval=2.3.1
• Test #8 - Conda dependency had pinned version number: bioconda::adapterremovalfixprefix=0.0.5
• Test #8 - Conda package is latest available: bioconda::adapterremovalfixprefix=0.0.5
• Test #8 - Conda dependency had pinned version number: bioconda::bwa=0.7.17
• Test #8 - Conda package is latest available: bioconda::bwa=0.7.17
• Test #8 - Conda dependency had pinned version number: bioconda::picard=2.22.9
• Test #8 - Conda dependency had pinned version number: bioconda::samtools=1.9
• Test #8 - Conda dependency had pinned version number: bioconda::dedup=0.12.6
• Test #8 - Conda package is latest available: bioconda::dedup=0.12.6
• Test #8 - Conda dependency had pinned version number: bioconda::angsd=0.933
• Test #8 - Conda package is latest available: bioconda::angsd=0.933
• Test #8 - Conda dependency had pinned version number: bioconda::circularmapper=1.93.5
• Test #8 - Conda package is latest available: bioconda::circularmapper=1.93.5
• Test #8 - Conda dependency had pinned version number: bioconda::gatk4=4.1.7.0
• Test #8 - Conda dependency had pinned version number: bioconda::qualimap=2.2.2d
• Test #8 - Conda package is latest available: bioconda::qualimap=2.2.2d
• Test #8 - Conda dependency had pinned version number: bioconda::vcf2genome=0.91
• Test #8 - Conda package is latest available: bioconda::vcf2genome=0.91
• Test #8 - Conda dependency had pinned version number: bioconda::damageprofiler=0.4.9
• Test #8 - Conda package is latest available: bioconda::damageprofiler=0.4.9
• Test #8 - Conda dependency had pinned version number: bioconda::multiqc=1.9
• Test #8 - Conda package is latest available: bioconda::multiqc=1.9
• Test #8 - Conda dependency had pinned version number: bioconda::pmdtools=0.60
• Test #8 - Conda package is latest available: bioconda::pmdtools=0.60
• Test #8 - Conda dependency had pinned version number: bioconda::bedtools=2.29.2
• Test #8 - Conda package is latest available: bioconda::bedtools=2.29.2
• Test #8 - Conda dependency had pinned version number: conda-forge::libiconv=1.15
• Test #8 - Conda package is latest available: conda-forge::libiconv=1.15
• Test #8 - Conda dependency had pinned version number: conda-forge::pigz=2.3.4
• Test #8 - Conda package is latest available: conda-forge::pigz=2.3.4
• Test #8 - Conda dependency had pinned version number: bioconda::sequencetools=1.4.0.6
• Test #8 - Conda package is latest available: bioconda::sequencetools=1.4.0.6
• Test #8 - Conda dependency had pinned version number: bioconda::preseq=2.0.3
• Test #8 - Conda package is latest available: bioconda::preseq=2.0.3
• Test #8 - Conda dependency had pinned version number: bioconda::fastp=0.20.1
• Test #8 - Conda package is latest available: bioconda::fastp=0.20.1
• Test #8 - Conda dependency had pinned version number: bioconda::bamutil=1.0.14
• Test #8 - Conda package is latest available: bioconda::bamutil=1.0.14
• Test #8 - Conda dependency had pinned version number: bioconda::mtnucratio=0.7
• Test #8 - Conda package is latest available: bioconda::mtnucratio=0.7
• Test #8 - Conda dependency had pinned version number: pysam=0.15.4
• Test #8 - Conda dependency had pinned version number: bioconda::kraken2=2.0.9beta
• Test #8 - Conda package is latest available: bioconda::kraken2=2.0.9beta
• Test #8 - Conda dependency had pinned version number: conda-forge::pandas=1.0.4
• Test #8 - Conda dependency had pinned version number: bioconda::freebayes=1.3.2
• Test #8 - Conda package is latest available: bioconda::freebayes=1.3.2
• Test #8 - Conda dependency had pinned version number: bioconda::sexdeterrmine=1.1.2
• Test #8 - Conda package is latest available: bioconda::sexdeterrmine=1.1.2
• Test #8 - Conda dependency had pinned version number: bioconda::multivcfanalyzer=0.85.2
• Test #8 - Conda package is latest available: bioconda::multivcfanalyzer=0.85.2
• Test #8 - Conda dependency had pinned version number: bioconda::hops=0.34
• Test #8 - Conda package is latest available: bioconda::hops=0.34
• Test #8 - Conda dependency had pinned version number: conda-forge::biopython=1.76
• Test #8 - Conda dependency had pinned version number: conda-forge::xopen=0.9.0
• Test #8 - Conda package is latest available: conda-forge::xopen=0.9.0
• Test #8 - Conda dependency had pinned version number: bioconda::bowtie2=2.4.1
• Test #8 - Conda package is latest available: bioconda::bowtie2=2.4.1
• 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 (138 files)
• Test #14 - Schema lint passed
• Test #14 - Schema title + description lint passed

Run details:

• nf-core/tools version 1.10.2
• Run at 2020-08-11 12:20:01

[jfy133]

Closing in preference of #538