Adapterremoval prefix fix

[jfy133]

nf-core/eager pull request

This re-adds ability to include singletons (unmergd reads) when running with DeDup as dedupper, by using the AdapterREmovalFixPrefix tool that adds R_ and L_ in addition to the Adpaterremoval prefix of M_ for merged reads.

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]

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]

nf-core lint overall result: Passed ✅

Updated for pipeline commit a706788

+| ✅ 144 tests passed       |+
!| ❗ 16 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 - Anaconda API timed out: https://api.anaconda.org/package/bioconda/multivcfanalyzer
• Test #8 - Conda package is not latest available: conda-forge::biopython=1.76, 1.78 available
• Test #8 - Anaconda API timed out: https://api.anaconda.org/package/bioconda/bowtie2

✅ 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 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 2020-11-09 10:16:34