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make sure one file is used in collapse step #36

Merged
merged 3 commits into from
Nov 11, 2020
Merged

make sure one file is used in collapse step #36

merged 3 commits into from
Nov 11, 2020

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lpantano
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@lpantano lpantano commented Feb 11, 2020 •
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this is related to UMI in the fastq files. Address:
#35

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/smrnaseq branch on the nf-core/test-datasets repo
  • Ensure the test suite passes (nextflow run . -profile test,docker).
  • 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: https://github.com/nf-core/smrnaseq/tree/master/.github/CONTRIBUTING.md

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nf-core lint overall result: Passed ✅

Posted for pipeline commit 1792272

+| ✅ 111 tests passed       |+
!| ❗ 21 tests had warnings |!
-| ❌  0 tests failed       |-

❗ Test warnings:

  • Test #5 - GitHub Actions AWS full test should test full datasets: /home/runner/work/smrnaseq/smrnaseq/.github/workflows/awsfulltest.yml
  • Test #8 - Conda package is not latest available: conda-forge::r-base=3.6.3, 4.0.3 available
  • Test #8 - Conda package is not latest available: conda-forge::r-statmod=1.4.32, 1.4.35 available
  • Test #8 - Conda package is not latest available: conda-forge::r-data.table=1.12.4, 1.13.2 available
  • Test #8 - Conda package is not latest available: conda-forge::r-gplots=3.0.1.1, 3.1.0 available
  • Test #8 - Conda package is not latest available: conda-forge::r-r.methodss3=1.7.1, 1.8.1 available
  • 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=3.1.1, 3.3.3 available
  • Test #8 - Conda package is not latest available: conda-forge::pymdown-extensions=6.0, 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: bioconda::trim-galore=0.6.5, 0.6.6 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::bowtie=1.2.3, 1.3.0 available
  • Test #8 - Conda package is not latest available: bioconda::htseq=0.11.3, 0.12.4 available
  • Test #8 - Conda package is not latest available: bioconda::seqkit=0.12.0, 0.14.0 available
  • Test #8 - Conda package is not latest available: bioconda::bioconductor-edger=3.26.5, 3.32.0 available
  • Test #8 - Conda package is not latest available: bioconda::bioconductor-limma=3.40.2, 3.46.0 available
  • Test #10 - TODO string found in test_full.config: Specify the paths to your full test data ( on nf-core/test-datasets or directly in repositories, e.g. SRA)
  • Test #10 - TODO string found in test_full.config: Give any required params for the test so that command line flags are not needed
  • Test #10 - TODO string found in awsfulltest.yml: You can customise AWS full pipeline tests as required
  • Test #10 - TODO string found in awstest.yml: You can customise CI pipeline run tests as required

✅ 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/smrnaseq:dev
  • Test #4 - Config manifest.version ends in dev: '1.1dev'
  • Test #5 - GitHub Actions 'branch' workflow is triggered for PRs to master: /home/runner/work/smrnaseq/smrnaseq/.github/workflows/branch.yml
  • Test #5 - GitHub Actions 'branch' workflow looks good: /home/runner/work/smrnaseq/smrnaseq/.github/workflows/branch.yml
  • Test #5 - GitHub Actions CI is triggered on expected events: /home/runner/work/smrnaseq/smrnaseq/.github/workflows/ci.yml
  • Test #5 - CI is building the correct docker image: docker build --no-cache . -t nfcore/smrnaseq:dev
  • Test #5 - CI is pulling the correct docker image: docker pull nfcore/smrnaseq:dev
  • Test #5 - CI is tagging docker image correctly: docker tag nfcore/smrnaseq:dev nfcore/smrnaseq:dev
  • Test #5 - Continuous integration checks minimum NF version: /home/runner/work/smrnaseq/smrnaseq/.github/workflows/ci.yml
  • Test #5 - GitHub Actions linting workflow is triggered on PR and push: /home/runner/work/smrnaseq/smrnaseq/.github/workflows/linting.yml
  • Test #5 - Continuous integration runs Markdown lint Tests: /home/runner/work/smrnaseq/smrnaseq/.github/workflows/linting.yml
  • Test #5 - Continuous integration runs nf-core lint Tests: /home/runner/work/smrnaseq/smrnaseq/.github/workflows/linting.yml
  • Test #5 - GitHub Actions AWS test is triggered on workflow_dispatch: /home/runner/work/smrnaseq/smrnaseq/.github/workflows/awstest.yml
  • Test #5 - GitHub Actions AWS full test is triggered only on published release and workflow_dispatch: /home/runner/work/smrnaseq/smrnaseq/.github/workflows/awsfulltest.yml
  • Test #6 - README Nextflow minimum version badge matched config. Badge: 19.10.0, Config: 19.10.0
  • Test #6 - README had a bioconda badge
  • Test #8 - Conda environment name was correct (nf-core-smrnaseq-1.1dev)
  • Test #8 - Conda dependency had pinned version number: conda-forge::r-base=3.6.3
  • Test #8 - Conda dependency had pinned version number: conda-forge::r-statmod=1.4.32
  • Test #8 - Conda dependency had pinned version number: conda-forge::r-data.table=1.12.4
  • Test #8 - Conda dependency had pinned version number: conda-forge::r-gplots=3.0.1.1
  • Test #8 - Conda dependency had pinned version number: conda-forge::r-r.methodss3=1.7.1
  • 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=3.1.1
  • Test #8 - Conda dependency had pinned version number: conda-forge::pymdown-extensions=6.0
  • Test #8 - Conda dependency had pinned version number: conda-forge::pygments=2.6.1
  • 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::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::trim-galore=0.6.5
  • Test #8 - Conda dependency had pinned version number: bioconda::samtools=1.9
  • Test #8 - Conda dependency had pinned version number: bioconda::bowtie=1.2.3
  • 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::mirtop=0.4.23
  • Test #8 - Conda package is latest available: bioconda::mirtop=0.4.23
  • Test #8 - Conda dependency had pinned version number: bioconda::seqcluster=1.2.7
  • Test #8 - Conda package is latest available: bioconda::seqcluster=1.2.7
  • Test #8 - Conda dependency had pinned version number: bioconda::htseq=0.11.3
  • Test #8 - Conda dependency had pinned version number: bioconda::fastx_toolkit=0.0.14
  • Test #8 - Conda package is latest available: bioconda::fastx_toolkit=0.0.14
  • Test #8 - Conda dependency had pinned version number: bioconda::seqkit=0.12.0
  • Test #8 - Conda dependency had pinned version number: bioconda::mirtrace=1.0.1
  • Test #8 - Conda package is latest available: bioconda::mirtrace=1.0.1
  • Test #8 - Conda dependency had pinned version number: bioconda::bioconductor-edger=3.26.5
  • Test #8 - Conda dependency had pinned version number: bioconda::bioconductor-limma=3.40.2
  • Test #8 - Conda dependency had pinned version number: bioconda::mirdeep2=2.0.1.2
  • Test #8 - Conda package is latest available: bioconda::mirdeep2=2.0.1.2
  • 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 (50 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 2020-11-11 07:58:53

@ewels ewels merged commit 3a0cb6c into dev Nov 11, 2020
@ewels ewels deleted the lpantano-patch-i35 branch November 11, 2020 11:38
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@ewels ewels ewels approved these changes

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@lpantano @ewels