olgabot/sourmash index #115

olgabot · 2020-10-28T15:26:20Z

nf-core/kmermaid pull request

Add option to do sourmash index.

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/kmermaid 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: CONTRIBUTING.md

github-actions · 2020-10-28T15:27:17Z

`nf-core lint` overall result: Failed ❌

Updated for pipeline commit a64765a

+| ✅ 110 tests passed       |+
!| ❗ 21 tests had warnings |!
-| ❌  1 tests failed       |-

❌ Test failures:

Test #9 - Could not find Dockerfile file string: FROM nfcore/base:1.11

❗ Test warnings:

Test #1 - File not found: .github/workflows/awstest.yml
Test #1 - File not found: .github/workflows/awsfulltest.yml
Test #6 - Found a bioconda environment.yml file but no badge in the README
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=2.5.2, 2.7.2 available
Test #8 - Conda package is not latest available: conda-forge::tqdm=4.43.0, 4.51.0 available
Test #8 - Conda package is not latest available: conda-forge::gxx_linux-64=7.3.0, 9.3.0 available
Test #8 - Conda package is not latest available: conda-forge::s3fs=0.4.2, 0.5.1 available
Test #8 - Conda package is not latest available: bioconda::samtools=1.10, 1.11 available
Test #8 - Conda package is not latest available: bioconda::pysam=0.16.0, 0.16.0.1 available
Test #8 - Conda package is not latest available: fastp=0.20.0, 0.20.1 available
Test #8 - Conda package is not latest available: matplotlib=3.1.1, 3.3.2 available
Test #8 - Conda package is not latest available: multiqc=1.8, 1.9 available
Test #8 - Conda package is not latest available: numpy=1.17.5, 1.19.2 available
Test #8 - Conda package is not latest available: pathos=0.2.5, 0.2.6 available
Test #8 - Conda package is not latest available: pip=20.0.2, 20.2.4 available
Test #8 - Conda package is not latest available: pytest=5.3.4, 6.1.1 available
Test #8 - Conda package is not latest available: sphinx=2.3.1, 3.2.1 available
Test #8 - Conda package is not latest available: sortmerna=2.1b, 4.2.0 available

✅ 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 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/kmermaid:dev
Test #4 - Config manifest.version ends in dev: '1.0.0dev'
Test #5 - GitHub Actions 'branch' workflow is triggered for PRs to master: /home/runner/work/kmermaid/kmermaid/.github/workflows/branch.yml
Test #5 - GitHub Actions 'branch' workflow looks good: /home/runner/work/kmermaid/kmermaid/.github/workflows/branch.yml
Test #5 - GitHub Actions CI is triggered on expected events: /home/runner/work/kmermaid/kmermaid/.github/workflows/ci.yml
Test #5 - CI is building the correct docker image: docker build --no-cache . -t nfcore/kmermaid:dev
Test #5 - CI is pulling the correct docker image: docker pull nfcore/kmermaid:dev
Test #5 - CI is tagging docker image correctly: docker tag nfcore/kmermaid:dev nfcore/kmermaid:dev
Test #5 - Continuous integration checks minimum NF version: /home/runner/work/kmermaid/kmermaid/.github/workflows/ci.yml
Test #5 - GitHub Actions linting workflow is triggered on PR and push: /home/runner/work/kmermaid/kmermaid/.github/workflows/linting.yml
Test #5 - Continuous integration runs Markdown lint Tests: /home/runner/work/kmermaid/kmermaid/.github/workflows/linting.yml
Test #5 - Continuous integration runs nf-core lint Tests: /home/runner/work/kmermaid/kmermaid/.github/workflows/linting.yml
Test #6 - README Nextflow minimum version badge matched config. Badge: 20.07.1, Config: 20.07.1
Test #8 - Conda environment name was correct (nf-core-kmermaid-1.0.0dev)
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=3.1.1
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=2.5.2
Test #8 - Conda dependency had pinned version number: conda-forge::tqdm=4.43.0
Test #8 - Conda dependency had pinned version number: conda-forge::gxx_linux-64=7.3.0
Test #8 - Conda dependency had pinned version number: conda-forge::s3fs=0.4.2
Test #8 - Conda dependency had pinned version number: bioconda::sourmash=3.5.0
Test #8 - Conda package is latest available: bioconda::sourmash=3.5.0
Test #8 - Conda dependency had pinned version number: bioconda::samtools=1.10
Test #8 - Conda dependency had pinned version number: bioconda::screed=1.0.4
Test #8 - Conda package is latest available: bioconda::screed=1.0.4
Test #8 - Conda dependency had pinned version number: bioconda::khmer=3.0.0a3
Test #8 - Conda package is latest available: bioconda::khmer=3.0.0a3
Test #8 - Conda dependency had pinned version number: bioconda::pysam=0.16.0
Test #8 - Conda dependency had pinned version number: anaconda::make=4.2.1
Test #8 - Conda package is latest available: anaconda::make=4.2.1
Test #8 - Conda dependency had pinned version number: alabaster=0.7.12
Test #8 - Conda package is latest available: alabaster=0.7.12
Test #8 - Conda dependency had pinned version number: fastp=0.20.0
Test #8 - Conda dependency had pinned version number: fastqc=0.11.9
Test #8 - Conda package is latest available: fastqc=0.11.9
Test #8 - Conda dependency had pinned version number: matplotlib=3.1.1
Test #8 - Conda dependency had pinned version number: multiqc=1.8
Test #8 - Conda dependency had pinned version number: numpy=1.17.5
Test #8 - Conda dependency had pinned version number: pathos=0.2.5
Test #8 - Conda dependency had pinned version number: pip=20.0.2
Test #8 - Conda dependency had pinned version number: pytest=5.3.4
Test #8 - Conda dependency had pinned version number: seqtk=1.3
Test #8 - Conda package is latest available: seqtk=1.3
Test #8 - Conda dependency had pinned version number: ska=1.0
Test #8 - Conda package is latest available: ska=1.0
Test #8 - Conda dependency had pinned version number: sphinx=2.3.1
Test #8 - Conda dependency had pinned version number: jupyter=1.0.0
Test #8 - Conda package is latest available: jupyter=1.0.0
Test #8 - Conda dependency had pinned version number: sortmerna=2.1b
Test #8 - Conda dependency had pinned version number: ripgrep=12.1.1
Test #8 - Conda package is latest available: ripgrep=12.1.1
Test #8 - Pip dependency had pinned version number: bam2fasta==1.0.8
Test #8 - PyPi package is latest available: 1.0.8
Test #8 - Pip dependency had pinned version number: sencha==1.0.3
Test #8 - PyPi package is latest available: 1.0.3

Run details:

nf-core/tools version 1.11
Run at 2020-10-28 15:49:22

pranathivemuri · 2020-10-29T18:38:48Z

skip_index should be added in nextflow_schema.json and conflicts should be resolved

pranathivemuri · 2020-10-29T18:39:52Z

main.nf

@@ -1422,6 +1440,35 @@ if (!params.split_kmer && !params.skip_compare && !params.skip_compute) {
  }
 }

+// If skip_compute is true, skip compare must be specified as true as well


this comment should be changed?

pranathivemuri · 2020-10-29T18:40:16Z

main.nf

@@ -1422,6 +1440,35 @@ if (!params.split_kmer && !params.skip_compare && !params.skip_compute) {
  }
 }

+// If skip_compute is true, skip compare must be specified as true as well
+if (!params.split_kmer && !params.skip_index && !params.skip_compute) {
+  process sourmash_index {


there is also sencha index can we name the folder sourmash_index?

olgabot · 2021-03-09T21:42:36Z

Closing for now as the desired behavior is more sourmash search. Will do sourmash index in a separate repo

olgabot added 3 commits October 28, 2020 08:25

Update changelog

ff6ad75

Add option to skip indexing

a4514de

Add sourmash index steap

86c4073

remove markdown_to_html.r to make linter happy

a64765a

olgabot mentioned this pull request Oct 29, 2020

Add option to query newly created signatures with "sourmash search" #118

Open

Update dockerfile

4c2b030

pranathivemuri reviewed Oct 29, 2020

View reviewed changes

pranathivemuri added 2 commits January 5, 2021 14:16

Merge branch 'dev' into olgabot/sourmash-index

b2bcbfd

Merge branch 'dev' into olgabot/sourmash-index

cd4162c

olgabot closed this Mar 9, 2021

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olgabot/sourmash index #115

olgabot/sourmash index #115

olgabot commented Oct 28, 2020 •

edited

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github-actions bot commented Oct 28, 2020 •

edited

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❌ Test failures:

❗ Test warnings:

✅ Tests passed:

Run details:

pranathivemuri commented Oct 29, 2020 •

edited

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pranathivemuri Oct 29, 2020

pranathivemuri Oct 29, 2020

olgabot commented Mar 9, 2021

olgabot/sourmash index #115

olgabot/sourmash index #115

Conversation

olgabot commented Oct 28, 2020 • edited Loading

nf-core/kmermaid pull request

PR checklist

github-actions bot commented Oct 28, 2020 • edited Loading

nf-core lint overall result: Failed ❌

❌ Test failures:

❗ Test warnings:

✅ Tests passed:

Run details:

pranathivemuri commented Oct 29, 2020 • edited Loading

pranathivemuri Oct 29, 2020

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olgabot commented Mar 9, 2021

olgabot commented Oct 28, 2020 •

edited

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github-actions bot commented Oct 28, 2020 •

edited

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`nf-core lint` overall result: Failed ❌

pranathivemuri commented Oct 29, 2020 •

edited

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