Update doc regarding bwa_index by maxibor · Pull Request #725 · nf-core/eager

maxibor · 2021-04-19T12:54:15Z

--bwa_index needs to be a directory path, not a filepath

PR checklist

This comment contains a description of changes (with reason).
Usage Documentation in docs/usage.md is updated.

github-actions · 2021-04-19T12:55:46Z

`nf-core lint` overall result: Passed ✅ ⚠️

Posted for pipeline commit 5fa6e53

+| ✅ 190 tests passed       |+
#| ❔   4 tests were ignored |#
!| ❗  23 tests had warnings |!

Details

❗ Test warnings:

conda_env_yaml - Conda dep outdated: conda-forge::python=3.7.3, 3.9.2 available
conda_env_yaml - Conda dep outdated: conda-forge::markdown=3.2.2, 3.3.4 available
conda_env_yaml - Conda dep outdated: conda-forge::pymdown-extensions=7.1, 8.1.1 available
conda_env_yaml - Conda dep outdated: conda-forge::pygments=2.6.1, 2.8.1 available
conda_env_yaml - Conda dep outdated: conda-forge::openjdk=8.0.144, 11.0.9.1 available
conda_env_yaml - Conda dep outdated: bioconda::adapterremoval=2.3.1, 2.3.2 available
conda_env_yaml - Conda dep outdated: bioconda::picard=2.22.9, 2.25.2 available
conda_env_yaml - Conda dep outdated: bioconda::samtools=1.9, 1.12 available
conda_env_yaml - Conda dep outdated: bioconda::angsd=0.933, 0.935 available
conda_env_yaml - Conda dep outdated: bioconda::gatk4=4.1.7.0, 4.2.0.0 available
conda_env_yaml - Conda dep outdated: bioconda::gatk=3.5, 3.8 available
conda_env_yaml - Conda dep outdated: bioconda::damageprofiler=0.4.9, 1.1 available
conda_env_yaml - Conda dep outdated: bioconda::bedtools=2.29.2, 2.30.0 available
conda_env_yaml - Conda dep outdated: conda-forge::libiconv=1.15, 1.16 available
conda_env_yaml - Conda dep outdated: bioconda::preseq=2.0.3, 3.1.2 available
conda_env_yaml - Conda dep outdated: bioconda::bamutil=1.0.14, 1.0.15 available
conda_env_yaml - Conda dep outdated: bioconda::pysam=0.15.4, 0.16.0 available
conda_env_yaml - Conda dep outdated: conda-forge::pandas=1.0.4, 1.2.4 available
conda_env_yaml - Conda dep outdated: bioconda::freebayes=1.3.2, 1.3.5 available
conda_env_yaml - Conda dep outdated: conda-forge::biopython=1.76, 1.78 available
conda_env_yaml - Conda dep outdated: conda-forge::xopen=0.9.0, 1.1.0 available
conda_env_yaml - Conda dep outdated: bioconda::mapdamage2=2.2.0, 2.2.1 available
conda_env_yaml - Conda dep outdated: bioconda::bbmap=38.87, 38.90 available

❔ Tests ignored:

files_unchanged - File ignored due to lint config: .github/CONTRIBUTING.md
files_unchanged - File ignored due to lint config: .github/ISSUE_TEMPLATE/bug_report.md
files_unchanged - File ignored due to lint config: docs/README.md
files_unchanged - File ignored due to lint config: assets/multiqc_config.yaml

✅ Tests passed:

files_exist - File found: .gitattributes
files_exist - File found: CHANGELOG.md
files_exist - File found: CODE_OF_CONDUCT.md
files_exist - File found: CODE_OF_CONDUCT.md
files_exist - File found: LICENSE or LICENSE.md or LICENCE or LICENCE.md
files_exist - File found: nextflow_schema.json
files_exist - File found: nextflow.config
files_exist - File found: README.md
files_exist - File found: .github/.dockstore.yml
files_exist - File found: .github/CONTRIBUTING.md
files_exist - File found: .github/ISSUE_TEMPLATE/bug_report.md
files_exist - File found: .github/ISSUE_TEMPLATE/config.yml
files_exist - File found: .github/ISSUE_TEMPLATE/feature_request.md
files_exist - File found: .github/markdownlint.yml
files_exist - File found: .github/PULL_REQUEST_TEMPLATE.md
files_exist - File found: .github/workflows/branch.yml
files_exist - File found: .github/workflows/ci.yml
files_exist - File found: .github/workflows/linting_comment.yml
files_exist - File found: .github/workflows/linting.yml
files_exist - File found: assets/email_template.html
files_exist - File found: assets/email_template.txt
files_exist - File found: assets/sendmail_template.txt
files_exist - File found: assets/nf-core-eager_logo.png
files_exist - File found: bin/markdown_to_html.py
files_exist - File found: docs/images/nf-core-eager_logo.png
files_exist - File found: docs/output.md
files_exist - File found: docs/README.md
files_exist - File found: docs/README.md
files_exist - File found: docs/usage.md
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files_exist - File found: lib/NfcoreSchema.groovy
files_exist - File found: main.nf
files_exist - File found: environment.yml
files_exist - File found: Dockerfile
files_exist - File found: conf/base.config
files_exist - File found: .github/workflows/awstest.yml
files_exist - File found: .github/workflows/awsfulltest.yml
files_exist - File not found check: Singularity
files_exist - File not found check: parameters.settings.json
files_exist - File not found check: bin/markdown_to_html.r
files_exist - File not found check: conf/aws.config
files_exist - File not found check: .github/workflows/push_dockerhub.yml
files_exist - File not found check: .travis.yml
nextflow_config - Config variable found: manifest.name
nextflow_config - Config variable found: manifest.nextflowVersion
nextflow_config - Config variable found: manifest.description
nextflow_config - Config variable found: manifest.version
nextflow_config - Config variable found: manifest.homePage
nextflow_config - Config variable found: timeline.enabled
nextflow_config - Config variable found: trace.enabled
nextflow_config - Config variable found: report.enabled
nextflow_config - Config variable found: dag.enabled
nextflow_config - Config variable found: process.cpus
nextflow_config - Config variable found: process.memory
nextflow_config - Config variable found: process.time
nextflow_config - Config variable found: params.outdir
nextflow_config - Config variable found: params.input
nextflow_config - Config variable found: manifest.mainScript
nextflow_config - Config variable found: timeline.file
nextflow_config - Config variable found: trace.file
nextflow_config - Config variable found: report.file
nextflow_config - Config variable found: dag.file
nextflow_config - Config variable found: process.container
nextflow_config - Config variable (correctly) not found: params.version
nextflow_config - Config variable (correctly) not found: params.nf_required_version
nextflow_config - Config variable (correctly) not found: params.container
nextflow_config - Config variable (correctly) not found: params.singleEnd
nextflow_config - Config variable (correctly) not found: params.igenomesIgnore
nextflow_config - Config variable (correctly) not found: params.name
nextflow_config - Config timeline.enabled had correct value: true
nextflow_config - Config report.enabled had correct value: true
nextflow_config - Config trace.enabled had correct value: true
nextflow_config - Config dag.enabled had correct value: true
nextflow_config - Config manifest.name began with nf-core/
nextflow_config - Config variable manifest.homePage began with https://github.com/nf-core/
nextflow_config - Config dag.file ended with .svg
nextflow_config - Config variable manifest.nextflowVersion started with >= or !>=
nextflow_config - Config process.container looks correct: nfcore/eager:dev
nextflow_config - Config manifest.version ends in dev: '2.3.4dev'
files_unchanged - .gitattributes matches the template
files_unchanged - CODE_OF_CONDUCT.md matches the template
files_unchanged - LICENSE matches the template
files_unchanged - .github/.dockstore.yml matches the template
files_unchanged - .github/ISSUE_TEMPLATE/config.yml matches the template
files_unchanged - .github/ISSUE_TEMPLATE/feature_request.md matches the template
files_unchanged - .github/markdownlint.yml matches the template
files_unchanged - .github/PULL_REQUEST_TEMPLATE.md matches the template
files_unchanged - .github/workflows/branch.yml matches the template
files_unchanged - .github/workflows/linting_comment.yml matches the template
files_unchanged - .github/workflows/linting.yml matches the template
files_unchanged - assets/email_template.html matches the template
files_unchanged - assets/email_template.txt matches the template
files_unchanged - assets/sendmail_template.txt matches the template
files_unchanged - assets/nf-core-eager_logo.png matches the template
files_unchanged - bin/markdown_to_html.py matches the template
files_unchanged - docs/images/nf-core-eager_logo.png matches the template
files_unchanged - lib/nfcore_external_java_deps.jar matches the template
files_unchanged - lib/NfcoreSchema.groovy matches the template
files_unchanged - .gitignore matches the template
files_unchanged - .github/workflows/push_dockerhub_dev.yml matches the template
files_unchanged - .github/workflows/push_dockerhub_release.yml matches the template
actions_ci - '.github/workflows/ci.yml' is triggered on expected events
actions_ci - CI is building the correct docker image: docker build --no-cache . -t nfcore/eager:dev
actions_ci - CI is pulling the correct docker image: docker pull nfcore/eager:dev
actions_ci - CI is tagging docker image correctly: docker tag nfcore/eager:dev nfcore/eager:dev
actions_ci - '.github/workflows/ci.yml' checks minimum NF version
actions_awstest - '.github/workflows/awstest.yml' is triggered correctly
actions_awsfulltest - .github/workflows/awsfulltest.yml is triggered correctly
actions_awsfulltest - .github/workflows/awsfulltest.yml does not use -profile test
readme - README Nextflow minimum version badge matched config. Badge: 20.07.1, Config: 20.07.1
readme - README had a bioconda badge
conda_env_yaml - Conda environment name was correct (nf-core-eager-2.3.4dev)
conda_env_yaml - Conda dep had pinned version number: conda-forge::python=3.7.3
conda_env_yaml - Conda dep had pinned version number: conda-forge::markdown=3.2.2
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conda_env_yaml - Conda dep had pinned version number: conda-forge::pygments=2.6.1
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conda_env_yaml - Conda package is the latest available: bioconda::rename=1.601
conda_env_yaml - Conda dep had pinned version number: conda-forge::openjdk=8.0.144
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conda_env_yaml - Conda package is the latest available: bioconda::fastqc=0.11.9
conda_env_yaml - Conda dep had pinned version number: bioconda::adapterremoval=2.3.1
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conda_env_yaml - Conda package is the latest available: bioconda::adapterremovalfixprefix=0.0.5
conda_env_yaml - Conda dep had pinned version number: bioconda::bwa=0.7.17
conda_env_yaml - Conda package is the latest available: bioconda::bwa=0.7.17
conda_env_yaml - Conda dep had pinned version number: bioconda::picard=2.22.9
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conda_env_yaml - Conda package is the latest available: bioconda::dedup=0.12.8
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conda_env_yaml - Conda package is the latest available: bioconda::circularmapper=1.93.5
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conda_env_yaml - Conda package is the latest available: bioconda::qualimap=2.2.2d
conda_env_yaml - Conda dep had pinned version number: bioconda::vcf2genome=0.91
conda_env_yaml - Conda package is the latest available: bioconda::vcf2genome=0.91
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conda_env_yaml - Conda package is the latest available: bioconda::multiqc=1.10.1
conda_env_yaml - Conda dep had pinned version number: bioconda::pmdtools=0.60
conda_env_yaml - Conda package is the latest available: bioconda::pmdtools=0.60
conda_env_yaml - Conda dep had pinned version number: bioconda::bedtools=2.29.2
conda_env_yaml - Conda dep had pinned version number: conda-forge::libiconv=1.15
conda_env_yaml - Conda dep had pinned version number: conda-forge::pigz=2.6
conda_env_yaml - Conda package is the latest available: conda-forge::pigz=2.6
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conda_env_yaml - Conda package is the latest available: bioconda::sequencetools=1.4.0.6
conda_env_yaml - Conda dep had pinned version number: bioconda::preseq=2.0.3
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conda_env_yaml - Conda package is the latest available: bioconda::fastp=0.20.1
conda_env_yaml - Conda dep had pinned version number: bioconda::bamutil=1.0.14
conda_env_yaml - Conda dep had pinned version number: bioconda::mtnucratio=0.7
conda_env_yaml - Conda package is the latest available: bioconda::mtnucratio=0.7
conda_env_yaml - Conda dep had pinned version number: bioconda::pysam=0.15.4
conda_env_yaml - Conda dep had pinned version number: bioconda::kraken2=2.1.1
conda_env_yaml - Conda package is the latest available: bioconda::kraken2=2.1.1
conda_env_yaml - Conda dep had pinned version number: conda-forge::pandas=1.0.4
conda_env_yaml - Conda dep had pinned version number: bioconda::freebayes=1.3.2
conda_env_yaml - Conda dep had pinned version number: bioconda::sexdeterrmine=1.1.2
conda_env_yaml - Conda package is the latest available: bioconda::sexdeterrmine=1.1.2
conda_env_yaml - Conda dep had pinned version number: bioconda::multivcfanalyzer=0.85.2
conda_env_yaml - Conda package is the latest available: bioconda::multivcfanalyzer=0.85.2
conda_env_yaml - Conda dep had pinned version number: bioconda::hops=0.35
conda_env_yaml - Conda package is the latest available: bioconda::hops=0.35
conda_env_yaml - Conda dep had pinned version number: conda-forge::biopython=1.76
conda_env_yaml - Conda dep had pinned version number: conda-forge::xopen=0.9.0
conda_env_yaml - Conda dep had pinned version number: bioconda::bowtie2=2.4.2
conda_env_yaml - Conda package is the latest available: bioconda::bowtie2=2.4.2
conda_env_yaml - Conda dep had pinned version number: bioconda::eigenstratdatabasetools=1.0.2
conda_env_yaml - Conda package is the latest available: bioconda::eigenstratdatabasetools=1.0.2
conda_env_yaml - Conda dep had pinned version number: bioconda::mapdamage2=2.2.0
conda_env_yaml - Conda dep had pinned version number: bioconda::bbmap=38.87
conda_dockerfile - Found all expected strings in Dockerfile file
pipeline_name_conventions - Name adheres to nf-core convention
template_strings - Did not find any Jinja template strings (146 files)
schema_lint - Schema lint passed
schema_lint - Schema title + description lint passed
schema_params - Schema matched params returned from nextflow config
actions_schema_validation - Workflow validation passed: linting_comment.yml
actions_schema_validation - Workflow validation passed: ci.yml
actions_schema_validation - Workflow validation passed: push_dockerhub_dev.yml
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: push_dockerhub_release.yml
actions_schema_validation - Workflow validation passed: branch.yml
actions_schema_validation - Workflow validation passed: awsfulltest.yml
actions_schema_validation - Workflow validation passed: awstest.yml
merge_markers - No merge markers found in pipeline files

Run details

nf-core/tools version 1.13.3
Run at 2021-04-25 14:48:21

jfy133

Is that any clearer?

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

jfy133

Please update CHANGELOG and GTG

github-actions · 2021-04-23T10:42:10Z

Markdown linting is failing

To keep the code consistent with lots of contributors, we run automated code consistency checks.
To fix this CI test, please run:

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github-actions · 2021-04-23T10:42:11Z

Markdown linting is failing

To keep the code consistent with lots of contributors, we run automated code consistency checks.
To fix this CI test, please run:

Install markdownlint-cli
- On Mac: brew install markdownlint-cli
- Everything else: Install npm then install markdownlint-cli (npm install -g markdownlint-cli)
Fix the markdown errors
- Automatically: markdownlint . --config .github/markdownlint.yml --fix
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update bwa_index doc

253507e

maxibor requested a review from jfy133 April 19, 2021 12:54

jfy133 linked an issue Apr 19, 2021 that may be closed by this pull request

--bwa_index help message confusing #724

Closed

jfy133 reviewed Apr 19, 2021

View reviewed changes

Comment thread nextflow_schema.json Outdated

Update nextflow_schema.json

7fe1501

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

jfy133 approved these changes Apr 19, 2021

View reviewed changes

maxibor added 2 commits April 23, 2021 10:39

update changelog

0e4ef9c

merge from PR

6709431

jfy133 added 3 commits April 25, 2021 16:45

Update CHANGELOG.md

806e247

Update CHANGELOG.md

bed1baf

Merge branch 'dev' into minor-doc-update

5fa6e53

jfy133 merged commit f1577ab into dev Apr 25, 2021

jfy133 deleted the minor-doc-update branch April 25, 2021 14:48

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Update doc regarding bwa_index#725

Update doc regarding bwa_index#725
jfy133 merged 7 commits intodevfrom
minor-doc-update

maxibor commented Apr 19, 2021

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github-actions Bot commented Apr 19, 2021 •

edited

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maxibor commented Apr 19, 2021

PR checklist

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nf-core lint overall result: Passed ✅ ⚠️

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github-actions Bot commented Apr 23, 2021

Markdown linting is failing

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Markdown linting is failing

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github-actions Bot commented Apr 19, 2021 •

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`nf-core lint` overall result: Passed ✅ ⚠️