Update doc regarding bwa_index #725

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conda_env_yaml - Conda dep outdated: conda-forge::python=3.7.3, 3.9.2 available
conda_env_yaml - Conda dep outdated: conda-forge::markdown=3.2.2, 3.3.4 available
conda_env_yaml - Conda dep outdated: conda-forge::pymdown-extensions=7.1, 8.1.1 available
conda_env_yaml - Conda dep outdated: conda-forge::pygments=2.6.1, 2.8.1 available
conda_env_yaml - Conda dep outdated: conda-forge::openjdk=8.0.144, 11.0.9.1 available
conda_env_yaml - Conda dep outdated: bioconda::adapterremoval=2.3.1, 2.3.2 available
conda_env_yaml - Conda dep outdated: bioconda::picard=2.22.9, 2.25.2 available
conda_env_yaml - Conda dep outdated: bioconda::samtools=1.9, 1.12 available
conda_env_yaml - Conda dep outdated: bioconda::angsd=0.933, 0.935 available
conda_env_yaml - Conda dep outdated: bioconda::gatk4=4.1.7.0, 4.2.0.0 available
conda_env_yaml - Conda dep outdated: bioconda::gatk=3.5, 3.8 available
conda_env_yaml - Conda dep outdated: bioconda::damageprofiler=0.4.9, 1.1 available
conda_env_yaml - Conda dep outdated: bioconda::bedtools=2.29.2, 2.30.0 available
conda_env_yaml - Conda dep outdated: conda-forge::libiconv=1.15, 1.16 available
conda_env_yaml - Conda dep outdated: bioconda::preseq=2.0.3, 3.1.2 available
conda_env_yaml - Conda dep outdated: bioconda::bamutil=1.0.14, 1.0.15 available
conda_env_yaml - Conda dep outdated: bioconda::pysam=0.15.4, 0.16.0 available
conda_env_yaml - Conda dep outdated: conda-forge::pandas=1.0.4, 1.2.4 available
conda_env_yaml - Conda dep outdated: bioconda::freebayes=1.3.2, 1.3.5 available
conda_env_yaml - Conda dep outdated: conda-forge::biopython=1.76, 1.78 available
conda_env_yaml - Conda dep outdated: conda-forge::xopen=0.9.0, 1.1.0 available
conda_env_yaml - Conda dep outdated: bioconda::mapdamage2=2.2.0, 2.2.1 available
conda_env_yaml - Conda dep outdated: bioconda::bbmap=38.87, 38.90 available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
files_exist - File found: lib/nfcore_external_java_deps.jar
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
conda_env_yaml - Conda dep had pinned version number: conda-forge::pymdown-extensions=7.1
conda_env_yaml - Conda dep had pinned version number: conda-forge::pygments=2.6.1
conda_env_yaml - Conda dep had pinned version number: bioconda::rename=1.601
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
conda_env_yaml - Conda dep had pinned version number: bioconda::fastqc=0.11.9
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
conda_env_yaml - Conda dep had pinned version number: bioconda::adapterremovalfixprefix=0.0.5
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
conda_env_yaml - Conda dep had pinned version number: bioconda::samtools=1.9
conda_env_yaml - Conda dep had pinned version number: bioconda::dedup=0.12.8
conda_env_yaml - Conda package is the latest available: bioconda::dedup=0.12.8
conda_env_yaml - Conda dep had pinned version number: bioconda::angsd=0.933
conda_env_yaml - Conda dep had pinned version number: bioconda::circularmapper=1.93.5
conda_env_yaml - Conda package is the latest available: bioconda::circularmapper=1.93.5
conda_env_yaml - Conda dep had pinned version number: bioconda::gatk4=4.1.7.0
conda_env_yaml - Conda dep had pinned version number: bioconda::gatk=3.5
conda_env_yaml - Conda dep had pinned version number: bioconda::qualimap=2.2.2d
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
conda_env_yaml - Conda dep had pinned version number: bioconda::damageprofiler=0.4.9
conda_env_yaml - Conda dep had pinned version number: bioconda::multiqc=1.10.1
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
conda_env_yaml - Conda dep had pinned version number: bioconda::sequencetools=1.4.0.6
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
conda_env_yaml - Conda dep had pinned version number: bioconda::fastp=0.20.1
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?

nextflow_schema.json

Co-authored-by: James A. Fellows Yates <[email protected]>

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:

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
- Manually resolve anything left from markdownlint . --config .github/markdownlint.yml

Once you push these changes the test should pass, and you can hide this comment 👍

We highly recommend setting up markdownlint in your code editor so that this formatting is done automatically on save. Ask about it on Slack for help!

Thanks again for your contribution!

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
- Manually resolve anything left from markdownlint . --config .github/markdownlint.yml

Once you push these changes the test should pass, and you can hide this comment 👍

We highly recommend setting up markdownlint in your code editor so that this formatting is done automatically on save. Ask about it on Slack for help!

Thanks again for your contribution!

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

nextflow_schema.json Outdated Show resolved Hide resolved

Update nextflow_schema.json

7fe1501

Co-authored-by: James A. Fellows Yates <[email protected]>

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

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

Uh oh!

Update doc regarding bwa_index #725

Update doc regarding bwa_index #725

Uh oh!

maxibor commented Apr 19, 2021

Uh oh!

github-actions bot commented Apr 19, 2021 •

edited

Loading

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

Uh oh!

jfy133 left a comment

Uh oh!

Uh oh!

jfy133 left a comment

Uh oh!

github-actions bot commented Apr 23, 2021

Uh oh!

github-actions bot commented Apr 23, 2021

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

3 participants

Update doc regarding bwa_index #725

Update doc regarding bwa_index #725

Uh oh!

Conversation

maxibor commented Apr 19, 2021

PR checklist

Uh oh!

github-actions bot commented Apr 19, 2021 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

nf-core lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

Uh oh!

jfy133 left a comment

Choose a reason for hiding this comment

Uh oh!

Uh oh!

jfy133 left a comment

Choose a reason for hiding this comment

Uh oh!

github-actions bot commented Apr 23, 2021

Markdown linting is failing

Uh oh!

github-actions bot commented Apr 23, 2021

Markdown linting is failing

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

3 participants

github-actions bot commented Apr 19, 2021 •

edited

Loading

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