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Added link to 1240k bedfile. Typo.#599

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TCLamnidis merged 1 commit intodevfrom
TCLamnidis-patch-1
Oct 30, 2020
Merged

Added link to 1240k bedfile. Typo.#599
TCLamnidis merged 1 commit intodevfrom
TCLamnidis-patch-1

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@TCLamnidis TCLamnidis commented Oct 30, 2020

nf-core/eager pull request

Small change to docs.

  • Added a link where users can download the 1240k bedfile when following the human popgen tutorial.
  • Corrected a small typo in said tutorial.

Now edited the correct branch.

PR checklist

  • This comment contains a description of changes (with reason)
  • 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

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github-actions Bot commented Oct 30, 2020

nf-core lint overall result: Passed ✅

Posted for pipeline commit 22f90a9

+| ✅ 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, 1.1.3 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 (136 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 2020-10-30 12:44:35

@TCLamnidis TCLamnidis requested a review from jfy133 October 30, 2020 12:46
@TCLamnidis TCLamnidis merged commit a99ce04 into dev Oct 30, 2020
@TCLamnidis TCLamnidis deleted the TCLamnidis-patch-1 branch October 30, 2020 14:23
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@jfy133 jfy133 jfy133 approved these changes

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@TCLamnidis @jfy133
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