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Rename "Stripping" section to "Host Removal" #531

Merged
merged 10 commits into from
Sep 30, 2020
Merged

Rename "Stripping" section to "Host Removal" #531

merged 10 commits into from
Sep 30, 2020

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olgabot
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@olgabot olgabot commented Jul 29, 2020

While many languages like Python have str.strip, str.rstrip, str.lstrip, it's not always clear to non-computer aficionados what it means. I think the flags make sense in context of their usage text, but I feel "Host Removal" is more clear to a new user. Happy to discuss!

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

@olgabot
Rename "Stripping" section to "Host Removal"
648ecd6 
While many languages like Python have `str.strip`, `str.rstrip`, `str.lstrip`, it's not always clear to non-computer aficionados what it means. I think the flags make sense in context of their usage text, but I feel "Host Removal" is more clear to a new user. Happy to discuss!
@jfy133
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jfy133 commented Jul 30, 2020

One for @maxibor. Do you think it is also worth updating this in script(-name)/process label etc.?

@apeltzer
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Guess we should - host-removal also makes it easier to understand, so I'm all for it ;-)

@jfy133 jfy133 requested a review from maxibor August 3, 2020 07:30
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jfy133 commented Sep 10, 2020

@maxibor thoughts, now you're back from holiday?

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maxibor commented Sep 10, 2020 •
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Sure, that sounds like a better name. I'm not too familiar yet with the new json-schema though, shouldn't the process name inmain.nf be renamed as well ?

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jfy133 commented Sep 10, 2020 •
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@maxibor yes we should change it everywhere in my opinion (including the script itself, if you're not too attached to the name). Do you want to take that over?

Alex or I can also update the schema once everything else is updated.

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github-actions bot commented Sep 15, 2020 •
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nf-core lint overall result: Passed ✅

Updated for pipeline commit da4a0a1

+| ✅ 145 tests passed       |+
!| ❗ 14 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::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, 2.23.4 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, 1.1.2 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
  • 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 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 (137 files)
  • Test #14 - Schema lint passed
  • Test #14 - Schema title + description lint passed

Run details:

  • nf-core/tools version 1.10.2
  • Run at 2020-09-27 16:29:03

TCLamnidis
TCLamnidis reviewed Sep 25, 2020
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apeltzer and others added 5 commits September 27, 2020 18:27
@apeltzer @TCLamnidis
Update .github/workflows/ci.yml
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Co-authored-by: Thiseas C. Lamnidis <[email protected]>
@apeltzer @TCLamnidis
Update docs/usage.md
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Co-authored-by: Thiseas C. Lamnidis <[email protected]>
@apeltzer @TCLamnidis
Update nextflow_schema.json
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Co-authored-by: Thiseas C. Lamnidis <[email protected]>
@apeltzer @TCLamnidis
Update docs/usage.md
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Co-authored-by: Thiseas C. Lamnidis <[email protected]>
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Update CHANGELOG.md
da4a0a1 
Co-authored-by: Thiseas C. Lamnidis <[email protected]>
@apeltzer apeltzer merged commit 9a19801 into dev Sep 30, 2020
@apeltzer apeltzer deleted the olgabot-patch-1 branch September 30, 2020 11:24
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Thanks everyone involved - @olgabot , @maxibor @jfy133 :-)

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@TCLamnidis TCLamnidis TCLamnidis approved these changes

@maxibor maxibor maxibor approved these changes

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@olgabot @jfy133 @apeltzer @maxibor @TCLamnidis