Master to dev by jfy133 · Pull Request #603 · nf-core/eager

jfy133 · 2020-11-04T10:53:38Z

nf-core/eager pull request

This gets patch stuff from master back into dev, but keeping the correct 2.3dev version numbers

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

Put 2.2.1 in better named branch

Patch 2.2.1

github-actions · 2020-11-04T11:07:03Z

`nf-core lint` overall result: Passed ✅

Updated for pipeline commit e0f2a88

+| ✅ 145 tests passed       |+
!| ❗ 15 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::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, 2.1.0 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: 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: '2.3.0dev'
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 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-2.3.0dev)
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 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::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 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 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 (135 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 2020-11-04 11:07:21

apeltzer

Should be fine

jfy133 added 17 commits October 23, 2020 14:54

Fix image issue in #591

31a47bc

Fix Issue #592

6e57f33

Merge pull request #593 from nf-core/2.2.1

46e6274

Put 2.2.1 in better named branch

Fix CHANGELOG linting

de6e4e0

Remove dockstore

613ebd6

Address #596

aa643e3

Version bump for patch

2ccbef9

Bump nf-core tools version

4693b8b

Fix nf-core 1.11 issue

7c28301

CHANGELOG

36ca27a

Address #582

d618e38

CHANGELOG

5b942dd

CHANGELOG

74e9255

Linting

fd58887

Changes from code review from @mashehu

6838a14

Missing header level

8ad3437

Merge pull request #594 from nf-core/patch-2.2.1

7971d89

Patch 2.2.1

jfy133 marked this pull request as draft November 4, 2020 10:53

jfy133 added 8 commits November 4, 2020 11:56

Reset 2.2.1 back up to dev

e13f80b

Update CHANGELOG.md

c073895

Push back up to 2.3

e8e693e

Bump back up to 2.3.0dev

9be472b

Update nextflow.config

31f9e0e

Remove Irina duplicate

4051c61

Merge branch 'dev' into master-to-dev

916ae4b

Typo

e0f2a88

jfy133 marked this pull request as ready for review November 4, 2020 11:09

apeltzer approved these changes Nov 4, 2020

View reviewed changes

jfy133 merged commit a6348fc into dev Nov 4, 2020

jfy133 deleted the master-to-dev branch November 4, 2020 12:15

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Master to dev#603

Master to dev#603
jfy133 merged 25 commits intodevfrom
master-to-dev

jfy133 commented Nov 4, 2020

Uh oh!

github-actions Bot commented Nov 4, 2020 •

edited

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❗ Test warnings:

✅ Tests passed:

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jfy133 commented Nov 4, 2020

nf-core/eager pull request

PR checklist

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nf-core lint overall result: Passed ✅

❗ Test warnings:

✅ Tests passed:

Run details:

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github-actions Bot commented Nov 4, 2020 •

edited

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`nf-core lint` overall result: Passed ✅