Rename "Stripping" section to "Host Removal" by olgabot · Pull Request #531 · nf-core/eager

olgabot · 2020-07-29T20:33:19Z

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

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 · 2020-07-30T07:18:44Z

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

apeltzer · 2020-07-31T11:23:49Z

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

jfy133 · 2020-09-10T08:36:07Z

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

maxibor · 2020-09-10T10:27:27Z

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 ?

jfy133 · 2020-09-10T18:22:23Z

@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.

Get latest dev version to check no flaky bam filtering

github-actions · 2020-09-15T06:42:39Z

`nf-core lint` overall result: Passed ✅

Updated for pipeline commit da4a0a1

+| ✅ 145 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 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

Co-authored-by: Thiseas C. Lamnidis <thisseass@gmail.com>

apeltzer · 2020-09-30T11:24:39Z

Thanks everyone involved - @olgabot , @maxibor @jfy133 :-)

jfy133 requested a review from maxibor August 3, 2020 07:30

jfy133 added 4 commits September 14, 2020 15:40

Replace all reference of strip with host removal (or equivalent)

b21fb60

Merge branch 'olgabot-patch-1' into olgabotpatch1-sync

2723a29

Update CHANGELOG.md

c2ad7a7

Merge pull request #556 from nf-core/olgabotpatch1-sync

a1bad01

Get latest dev version to check no flaky bam filtering