Main nf whitespace #28

ewels · 2021-04-14T22:30:05Z

Fix a lot of the things that I requested changes for in #19

Stuff like whitespace fixes, command line breaks and squiggly brackets is dull to fix up but I think important. I thought it was quicker to fix these things myself than it would be to try to nitpick every instance.

I tried to keep my commits fairly logical so that you can view individual changes and not just be swamped by the whitespace changes. Let me know if you have any thoughts / concerns about any of this.

github-actions · 2021-04-14T22:31:21Z

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

Posted for pipeline commit 04e34f0

+| ✅ 148 tests passed       |+
!| ❗   2 tests had warnings |!

❗ Test warnings:

nextflow_config - Config manifest.version should end in dev: '1.0.0'
pipeline_todos - TODO string in README.md: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi.

✅ 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-pgdb_logo.png
files_exist - File found: bin/markdown_to_html.py
files_exist - File found: docs/images/nf-core-pgdb_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/pgdb:1.0.0
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/CONTRIBUTING.md matches the template
files_unchanged - .github/ISSUE_TEMPLATE/bug_report.md 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-pgdb_logo.png matches the template
files_unchanged - bin/markdown_to_html.py matches the template
files_unchanged - docs/images/nf-core-pgdb_logo.png matches the template
files_unchanged - docs/README.md 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
files_unchanged - assets/multiqc_config.yaml 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/pgdb:1.0.0
actions_ci - CI is pulling the correct docker image: docker pull nfcore/pgdb:dev
actions_ci - CI is tagging docker image correctly: docker tag nfcore/pgdb:dev nfcore/pgdb:1.0.0
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: 20.04.0, Config: 20.04.0
readme - README had a bioconda badge
conda_env_yaml - Conda environment name was correct (nf-core-pgdb-1.0.0)
conda_env_yaml - Conda dep had pinned version number: conda-forge::python=3.9.2
conda_env_yaml - Conda package is the latest available: conda-forge::python=3.9.2
conda_env_yaml - Conda dep had pinned version number: conda-forge::markdown=3.3.4
conda_env_yaml - Conda package is the latest available: conda-forge::markdown=3.3.4
conda_env_yaml - Conda dep had pinned version number: conda-forge::pymdown-extensions=8.1.1
conda_env_yaml - Conda package is the latest available: conda-forge::pymdown-extensions=8.1.1
conda_env_yaml - Conda dep had pinned version number: conda-forge::pygments=2.8.1
conda_env_yaml - Conda package is the latest available: conda-forge::pygments=2.8.1
conda_env_yaml - Conda dep had pinned version number: conda-forge::coreutils=8.31
conda_env_yaml - Conda package is the latest available: conda-forge::coreutils=8.31
conda_env_yaml - Conda dep had pinned version number: conda-forge::git-lfs=2.13.3
conda_env_yaml - Conda package is the latest available: conda-forge::git-lfs=2.13.3
conda_env_yaml - Conda dep had pinned version number: conda-forge::git=2.30.2
conda_env_yaml - Conda package is the latest available: conda-forge::git=2.30.2
conda_env_yaml - Conda dep had pinned version number: bioconda::gffread=0.12.1
conda_env_yaml - Conda package is the latest available: bioconda::gffread=0.12.1
conda_env_yaml - Conda dep had pinned version number: bioconda::pypgatk=0.0.19
conda_env_yaml - Conda package is the latest available: bioconda::pypgatk=0.0.19
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 (55 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.yml
actions_schema_validation - Workflow validation passed: branch.yml
actions_schema_validation - Workflow validation passed: awstest.yml
actions_schema_validation - Workflow validation passed: awsfulltest.yml
actions_schema_validation - Workflow validation passed: push_dockerhub_dev.yml
actions_schema_validation - Workflow validation passed: ci.yml
actions_schema_validation - Workflow validation passed: linting_comment.yml
actions_schema_validation - Workflow validation passed: push_dockerhub_release.yml
merge_markers - No merge markers found in pipeline files

Run details

nf-core/tools version 1.13.3
Run at 2021-04-14 23:06:25

…for --ensembl_name

ewels added 5 commits April 14, 2021 23:59

Tabs to spaces

41ed3ac

Sort out indentation in main.nf

1442057

Remove double-header, move summary to top of main.nf

ccb1053

Remove unused ZCAT, clone into cwd

80a2ea7

Strip {} from lots of variables

8a2bc98

ewels added 10 commits April 15, 2021 00:35

nextflow.config whitespace, config_profile_name

d6b5e02

Don't limit resources for test_full, drop single_end

48e4078

baseDir -> projectDir

d9e93ab

Added missing config_profile_name to schema

015f767

Move params.cbioportal_study_id initialisation into nextflow.config

8c0893b

Space after // comment

e843382

Drop duplicate .Rprofile creation from Dockerfile

6d08b56

--taxonomy not used anywhere, replaced in schema and nextflow.config …

37b2fd6

…for --ensembl_name

Finish stripping custom_runName

bb32a88

Use the pipeline summary from the schema

04e34f0

ypriverol self-requested a review April 15, 2021 05:39

ypriverol approved these changes Apr 15, 2021

View reviewed changes

ypriverol merged commit 9607a8e into nf-core:dev Apr 15, 2021

ewels deleted the main-nf-whitespace branch April 15, 2021 07:48

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Main nf whitespace #28

Main nf whitespace #28

ewels commented Apr 14, 2021 •

edited

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github-actions bot commented Apr 14, 2021 •

edited

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❗ Test warnings:

✅ Tests passed:

Run details

Main nf whitespace #28

Main nf whitespace #28

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ewels commented Apr 14, 2021 • edited Loading

github-actions bot commented Apr 14, 2021 • edited Loading

nf-core lint overall result: Passed ✅ ⚠️

❗ Test warnings:

✅ Tests passed:

Run details

ewels commented Apr 14, 2021 •

edited

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github-actions bot commented Apr 14, 2021 •

edited

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