Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Malt sam output #557

Merged
merged 3 commits into from
Sep 25, 2020
Merged

Malt sam output #557

merged 3 commits into from
Sep 25, 2020

Conversation

jfy133
Copy link
Member

@jfy133 jfy133 commented Sep 15, 2020 •
edited

nf-core/eager pull request

This adds optional exporting of SAM files alongside RMA6 files when running MALT. To close #552

Note I am not adding all possible flags because in most cases can be modified after the fact, and this is dangerous territory already due to large file size (see warning in usage.md)

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

@jfy133 jfy133 requested a review from a team September 15, 2020 08:27
@github-actions
Copy link

nf-core lint overall result: Passed ✅

Posted for pipeline commit eb84ad0

+| ✅ 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, 2.7.0 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 2020-09-15 08:28:15

@jfy133 jfy133 linked an issue Sep 15, 2020 that may be closed by this pull request
MALT output format options #552
Closed
@jfy133 jfy133 merged commit cf41572 into dev Sep 25, 2020
@jfy133 jfy133 deleted the malt-sam-output branch September 25, 2020 13:20
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@TCLamnidis TCLamnidis TCLamnidis approved these changes

Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.

MALT output format options
2 participants
@jfy133 @TCLamnidis