Add integrated GATK 3.5 :muscle: by jfy133 · Pull Request #609 · nf-core/eager

jfy133 · 2020-11-13T11:37:08Z

nf-core/eager pull request

This adds the GATK3.5 conda environment and deprecates --gatk_ug_jar accordingly to close #602

It also drops the version down to the next patch as a few more bugs have been identified so will need to fix these soon.

And bonus docs typo fix (thanks @scarlhoff!)

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

github-actions · 2020-11-13T11:37:24Z

Hi @jfy133,

It looks like this pull-request is has been made against the nf-core/eager master branch.
The master branch on nf-core repositories should always contain code from the latest release.
Because of this, PRs to master are only allowed if they come from the nf-core/eager dev branch.

You do not need to close this PR, you can change the target branch to dev by clicking the "Edit" button at the top of this page.

Thanks again for your contribution!

github-actions · 2020-11-13T11:38:23Z

`nf-core lint` overall result: Passed ✅

Updated for pipeline commit cf20fcb

+| ✅ 145 tests passed       |+
!| ❗ 17 tests had warnings |!
-| ❌  0 tests failed       |-

Details

❗ Test warnings:

Test #8 - Conda package is not latest available: conda-forge::python=3.7.3, 3.9.0 available
Test #8 - Conda package is not latest available: conda-forge::markdown=3.2.2, 3.3.3 available
Test #8 - Conda package is not latest available: conda-forge::pymdown-extensions=7.1, 8.0.1 available
Test #8 - Conda package is not latest available: conda-forge::pygments=2.6.1, 2.7.2 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, 2.23.8 available
Test #8 - Conda package is not latest available: bioconda::samtools=1.9, 1.11 available
Test #8 - Conda package is not latest available: bioconda::gatk4=4.1.7.0, 4.1.9.0 available
Test #8 - Conda package is not latest available: bioconda::gatk=3.5, 3.8 available
Test #8 - Conda package is not latest available: bioconda::damageprofiler=0.4.9, 1.1 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: bioconda::pysam=0.15.4, 0.16.0.1 available
Test #8 - Conda package is not latest available: bioconda::kraken2=2.0.9beta, 2.1.1 available
Test #8 - Conda package is not latest available: conda-forge::pandas=1.0.4, 1.1.4 available
Test #8 - Conda package is not latest available: conda-forge::biopython=1.76, 1.78 available
Test #8 - Conda package is not latest available: conda-forge::xopen=0.9.0, 1.0.1 available
Test #8 - Conda package is not latest available: bioconda::bowtie2=2.4.1, 2.4.2 available

✅ 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/eager:dev
Test #4 - Config manifest.version ends in dev: '2.2.2dev'
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 workflow_dispatch: /home/runner/work/eager/eager/.github/workflows/awstest.yml
Test #5 - GitHub Actions AWS full test is triggered only on published release and workflow_dispatch: /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-2.2.2dev)
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 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 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=0.12.7
Test #8 - Conda package is latest available: bioconda::dedup=0.12.7
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::gatk=3.5
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: bioconda::pysam=0.15.4
Test #8 - Conda dependency had pinned version number: 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 dependency had pinned version number: bioconda::bowtie2=2.4.1
Test #8 - Conda dependency had pinned version number: bioconda::eigenstratdatabasetools=1.0.2
Test #8 - Conda package is latest available: bioconda::eigenstratdatabasetools=1.0.2
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 (137 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 1.11
Run at 2020-11-17 08:01:26

Remove GATK manual Jar specification and drop version for next patch

25a70d6

jfy133 changed the base branch from master to dev November 13, 2020 11:37

jfy133 requested a review from a team November 13, 2020 11:38

jfy133 added 7 commits November 13, 2020 12:41

Remove leftover run:

91721d3

Actually remove use of the jars 🤦

eea2dd0

Update usage.md

2666385

Update nextflow_schema.json

dbca8ea

Merge branch 'dev' into gatk3

13687a5

Fix GHA fails due to deprecated variables

f3c8be4

Merge branch 'gatk3' of github.com:nf-core/eager into gatk3

cf20fcb

apeltzer approved these changes Nov 17, 2020

View reviewed changes

apeltzer merged commit 23be10d into dev Nov 17, 2020

jfy133 deleted the gatk3 branch November 17, 2020 09:57

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Add integrated GATK 3.5 💪#609

Add integrated GATK 3.5 💪#609
apeltzer merged 8 commits intodevfrom
gatk3

jfy133 commented Nov 13, 2020 •

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jfy133 commented Nov 13, 2020 • edited Loading Uh oh! There was an error while loading. Please reload this page.

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nf-core/eager pull request

PR checklist

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nf-core lint overall result: Passed ✅

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jfy133 commented Nov 13, 2020 •

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`nf-core lint` overall result: Passed ✅