Bump DeDup for stats fix and DamageProfiler to latest version by jfy133 · Pull Request #565 · nf-core/eager

jfy133 · 2020-09-28T12:13:56Z

nf-core/eager pull request

This bumps DeDup to latest bug fix version to close #560 .

This also adds the number of covered by each individual and total SNPs in the eigenstrat genotype dataset produced by pileupcaller, when that is used for genotyping, in the final MutiQC report.

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 · 2020-09-28T12:14:13Z

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 · 2020-09-28T12:15:03Z

`nf-core lint` overall result: Passed ✅

Updated for pipeline commit 2d289df

+| ✅ 147 tests passed       |+
!| ❗ 14 tests had warnings |!
-| ❌  0 tests failed       |-

Details

❗ 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, 8.0.1 available
Test #8 - Conda package is not latest available: conda-forge::pygments=2.6.1, 2.7.1 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, 2.23.6 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, 4.1.8.1 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: bioconda::pysam=0.15.4, 0.16.0.1 available
Test #8 - Conda package is not latest available: conda-forge::pandas=1.0.4, 1.1.3 available
Test #8 - Conda package is not latest available: conda-forge::biopython=1.76, 1.78 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
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Test #1 - File found: main.nf
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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
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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
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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
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Test #8 - Conda dependency had pinned version number: conda-forge::openjdk=8.0.144
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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
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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
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Test #8 - Conda dependency had pinned version number: bioconda::vcf2genome=0.91
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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
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Test #8 - Conda dependency had pinned version number: bioconda::bedtools=2.29.2
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Test #8 - Conda dependency had pinned version number: conda-forge::pigz=2.3.4
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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
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Test #8 - Conda package is latest available: bioconda::bamutil=1.0.14
Test #8 - Conda dependency had pinned version number: bioconda::mtnucratio=0.7
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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
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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
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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
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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 #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 (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 2020-10-06 14:51:41

jfy133 · 2020-09-29T14:39:37Z

Waiting for @TCLamnidis 's additions

…tools mqc module is released.

TCLamnidis · 2020-10-05T14:42:45Z

required version of eigenstratdatabasetools is not yet updated in bioconda. should be up soon. Will then update README and CHANGELOG to force checks to restart

jfy133

One comment but otherwise looks good.

Update changelog/readme and feel free to approve and merge @TCLamnidis

…process

Get DeDup version with reporting bugfix

0311d4b

jfy133 changed the base branch from master to dev September 28, 2020 12:14

Update CHANGELOG.md

b6549b2

jfy133 changed the title ~~Dedup~~ Bump DeDup for stats fix Sep 28, 2020

Update environment.yml

4025b3a

jfy133 changed the title ~~Bump DeDup for stats fix~~ Bump DeDup for stats fix and DamageProfiler to latest version Sep 28, 2020

Reverting DamageProfiler version due to Java version incompatibility

d8d46c4

jfy133 marked this pull request as draft September 29, 2020 14:39

TCLamnidis added 5 commits October 5, 2020 16:35

Added eigenstrat_snp_coverage process

1445062

Parsing version of eigenstrat_snp_coverage

b04a619

Small script to make MQC custom-content JSON until eigenstratdatabase…

efb8422

…tools mqc module is released.

Added eigenstrat_snp_coverage columns

30ef521

Added eigenstratdatabasetools v1.0.2

108e447

Update environment.yml

b728a6d

jfy133 commented Oct 6, 2020

View reviewed changes

Comment thread main.nf

TCLamnidis added 4 commits October 6, 2020 16:04

Added eigenstrat_snp_coverage

e420339

Update README.md

f90e5ba

Added info on eigenstrat_snp_coverage columns of GeneralStatsTable

6383d3f

Added explanation of the extra code block in eigenstrat_snp_coverage …

2d289df

…process

TCLamnidis marked this pull request as ready for review October 6, 2020 16:49

TCLamnidis approved these changes Oct 6, 2020

View reviewed changes

TCLamnidis merged commit aff33ad into dev Oct 6, 2020

apeltzer deleted the dedup branch October 6, 2020 19:49

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Bump DeDup for stats fix and DamageProfiler to latest version#565

Bump DeDup for stats fix and DamageProfiler to latest version#565
TCLamnidis merged 14 commits intodevfrom
dedup

jfy133 commented Sep 28, 2020 •

edited by TCLamnidis

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nf-core/eager pull request

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nf-core lint overall result: Passed ✅

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✅ Tests passed:

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jfy133 commented Sep 28, 2020 •

edited by TCLamnidis

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`nf-core lint` overall result: Passed ✅