Docs and schema update #538

jfy133 · 2020-08-11T12:03:38Z

nf-core/eager pull request

This PR condenses all docs into usage.md to make sure all docs are avaliable on the nf-core website. It also copies all docs into the schema help boxes and syncronises the order.

The only page not included is code_contribution.md as I don't think that is necessary given a developer would be working here anyway.

Also 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

Co-authored-by: James A. Fellows Yates <[email protected]>

github-actions · 2020-08-11T12:04:58Z

`nf-core lint` overall result: Passed ✅

Updated for pipeline commit c5363b3

+| ✅ 146 tests passed       |+
!| ❗ 13 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::pymdown-extensions=7.1, 8.0 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: bioconda::damageprofiler=0.4.9, 0.5.0 available
Test #8 - Conda package is not latest available: conda-forge::libiconv=1.15, 1.16 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, 1.1.1 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 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 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 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 (136 files)
Test #14 - Schema lint passed
Test #14 - Schema title + description lint passed

Run details:

nf-core/tools version 1.10.2
Run at 2020-09-01 06:45:46

…cs-schema-update

jfy133 · 2020-09-01T06:48:13Z

Due to time constraints, Pathogen tutorial will come later.

jfy133 and others added 30 commits July 20, 2020 15:41

Started work on tutorials

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Finished first draft of tutorail_metagenomic.md

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Update tutorial_metagenomic.md

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Update CHANGELOG.md

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Linting

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Actually linting

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Fix emoji

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Merge remote-tracking branch 'origin/dev' into example-tutorials

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Typo

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Added tutorial for human popgen

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Minor changes. Phrasing and typos.

c1c2ea4

Tweaks to metagenomics tutorial

b9b6be2

Corrected title. Linting

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Update docs/tutorial_human_popgen.md

e9a0fe2

Co-authored-by: James A. Fellows Yates <[email protected]>

Update docs/tutorial_human_popgen.md

1f0761b

Co-authored-by: James A. Fellows Yates <[email protected]>

Update docs/tutorial_human_popgen.md

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Co-authored-by: James A. Fellows Yates <[email protected]>

Update docs/tutorial_human_popgen.md

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Co-authored-by: James A. Fellows Yates <[email protected]>

Update docs/tutorial_human_popgen.md

41fd4cc

Co-authored-by: James A. Fellows Yates <[email protected]>

Update docs/tutorial_human_popgen.md

d7c10ee

Co-authored-by: James A. Fellows Yates <[email protected]>

Update docs/tutorial_human_popgen.md

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Co-authored-by: James A. Fellows Yates <[email protected]>

Update docs/tutorial_human_popgen.md

76c0830

Co-authored-by: James A. Fellows Yates <[email protected]>

Addressing Jame's review.

d97dc9c

Linting...

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Changed dirname from screening to preprossessing

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Added human popgen tutorial link

85e1c12

Typo

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Update docs/tutorial_human_popgen.md

9d5004c

Co-authored-by: James A. Fellows Yates <[email protected]>

Update docs/tutorial_human_popgen.md

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Co-authored-by: James A. Fellows Yates <[email protected]>

Additional fixes

1d09fa9

Added citation for effect of mt/nuc ratio on contamination estimates

01ef742

jfy133 added 4 commits August 11, 2020 13:41

update docs for display on nf-co.re

8b37e43

Update schema and docs for nf-co.re

85c8a93

update README to remove references to old docs files

ac14fcb

Bump circular mapper

ff64b53

jfy133 changed the title ~~Docs schema update~~ Docs and schema update Aug 11, 2020

jfy133 requested review from apeltzer, TCLamnidis and maxulysse and removed request for apeltzer August 11, 2020 12:03

jfy133 added 5 commits August 11, 2020 14:05

Linting

8ab3f77

Update docs README

7b7d720

Typo fix

ae3869b

Merge branch 'example-tutorials' into docs-schema-update

6777db6

Combine new tutorials into usage.md

6c48ef4

jfy133 marked this pull request as draft August 11, 2020 12:48

jfy133 mentioned this pull request Aug 11, 2020

Example tutorials #520

Closed

8 tasks

jfy133 linked an issue Aug 11, 2020 that may be closed by this pull request

Make a few tutorials on how to run for different contexts #466

Closed

5 tasks

jfy133 added 3 commits September 1, 2020 08:38

Move pathogen screening out of usage

03186ed

Linting

0aa1760

Merge branch 'dev' into docs-schema-update

d3c718f

jfy133 marked this pull request as ready for review September 1, 2020 06:42

jfy133 added 3 commits September 1, 2020 08:42

More linting

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Merge branch 'docs-schema-update' of github.com:nf-core/eager into do…

8432209

…cs-schema-update

Linting again

c5363b3

apeltzer approved these changes Sep 1, 2020

View reviewed changes

apeltzer merged commit baa0d60 into dev Sep 1, 2020

jfy133 deleted the docs-schema-update branch September 25, 2020 12:36

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Docs and schema update #538

Docs and schema update #538

jfy133 commented Aug 11, 2020 •

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github-actions bot commented Aug 11, 2020 •

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❗ Test warnings:

✅ Tests passed:

Run details:

jfy133 commented Sep 1, 2020

Docs and schema update #538

Docs and schema update #538

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jfy133 commented Aug 11, 2020 • edited Loading

nf-core/eager pull request

PR checklist

github-actions bot commented Aug 11, 2020 • edited Loading

nf-core lint overall result: Passed ✅

❗ Test warnings:

✅ Tests passed:

Run details:

jfy133 commented Sep 1, 2020

jfy133 commented Aug 11, 2020 •

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github-actions bot commented Aug 11, 2020 •

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`nf-core lint` overall result: Passed ✅