Pre-release fixes and syncing with latest DSL2 pipeline template #38

drpatelh · 2021-05-28T12:52:40Z

No description provided.

github-actions · 2021-05-28T12:57:12Z

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

Posted for pipeline commit bad6c78

+| ✅ 110 tests passed       |+
#| ❔  14 tests were ignored |#
!| ❗  42 tests had warnings |!

Details

❗ Test warnings:

files_exist - File not found: environment.yml
files_exist - File not found: Dockerfile
nextflow_config - Config variable not found: process.container
params_used - Config variable not found in main.nf: params.input
params_used - Config variable not found in main.nf: params.reference
params_used - Config variable not found in main.nf: params.trim
params_used - Config variable not found in main.nf: params.save_trimmed_fail
params_used - Config variable not found in main.nf: params.adapter_file
params_used - Config variable not found in main.nf: params.subsampling_off
params_used - Config variable not found in main.nf: params.subsampling_depth_cutoff
params_used - Config variable not found in main.nf: params.genome_size
params_used - Config variable not found in main.nf: params.remove_recombination
params_used - Config variable not found in main.nf: params.non_GATC_threshold
params_used - Config variable not found in main.nf: params.rapidnj
params_used - Config variable not found in main.nf: params.fasttree
params_used - Config variable not found in main.nf: params.iqtree
params_used - Config variable not found in main.nf: params.raxmlng
params_used - Config variable not found in main.nf: params.multiqc_config
params_used - Config variable not found in main.nf: params.multiqc_title
params_used - Config variable not found in main.nf: params.outdir
params_used - Config variable not found in main.nf: params.tracedir
params_used - Config variable not found in main.nf: params.publish_dir_mode
params_used - Config variable not found in main.nf: params.email
params_used - Config variable not found in main.nf: params.email_on_fail
params_used - Config variable not found in main.nf: params.plaintext_email
params_used - Config variable not found in main.nf: params.max_multiqc_email_size
params_used - Config variable not found in main.nf: params.skip_multiqc
params_used - Config variable not found in main.nf: params.enable_conda
params_used - Config variable not found in main.nf: params.validate_params
params_used - Config variable not found in main.nf: params.monochrome_logs
params_used - Config variable not found in main.nf: params.help
params_used - Config variable not found in main.nf: params.singularity_pull_docker_container
params_used - Config variable not found in main.nf: params.hostnames
params_used - Config variable not found in main.nf: params.config_profile_description
params_used - Config variable not found in main.nf: params.config_profile_contact
params_used - Config variable not found in main.nf: params.config_profile_url
params_used - Config variable not found in main.nf: params.max_memory
params_used - Config variable not found in main.nf: params.max_cpus
params_used - Config variable not found in main.nf: params.max_time
readme - README did not have a Nextflow minimum version badge.
pipeline_todos - TODO string in README.md: Add citation for pipeline after first release. Uncomment lines below, update Zenodo doi and badge at the top of this file.
pipeline_todos - TODO string in WorkflowMain.groovy: Add Zenodo DOI for pipeline after first release

❔ Tests ignored:

files_exist - File is ignored: .github/markdownlint.yml
files_exist - File is ignored: bin/markdown_to_html.py
files_unchanged - File does not exist: .github/markdownlint.yml
files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
files_unchanged - File ignored due to lint config: .github/workflows/linting.yml
files_unchanged - File ignored due to lint config: assets/sendmail_template.txt
files_unchanged - File does not exist: bin/markdown_to_html.py
files_unchanged - File ignored due to lint config: docs/README.md
files_unchanged - File ignored due to lint config: lib/NfcoreSchema.groovy
files_unchanged - File does not exist: .github/workflows/push_dockerhub_dev.yml
files_unchanged - File does not exist: .github/workflows/push_dockerhub_release.yml
actions_awsfulltest - actions_awsfulltest
conda_env_yaml - No environment.yml file found - skipping conda_env_yaml test
conda_dockerfile - No environment.yml / Dockerfile file found - skipping conda_dockerfile test

✅ 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/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-bactmap_logo.png
files_exist - File found: docs/images/nf-core-bactmap_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: 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: params.show_hidden_params
nextflow_config - Config variable found: params.schema_ignore_params
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 (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 manifest.version ends in dev: '1.0dev'
nextflow_config - Config params.custom_config_version is set to master
nextflow_config - Config params.custom_config_base is set to https://raw.githubusercontent.com/nf-core/configs/master
nextflow_config - Lines for loading custom profiles found
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/workflows/branch.yml matches the template
files_unchanged - .github/workflows/linting_comment.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/nf-core-bactmap_logo.png matches the template
files_unchanged - docs/images/nf-core-bactmap_logo.png matches the template
files_unchanged - lib/nfcore_external_java_deps.jar matches the template
files_unchanged - .gitignore 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 - '.github/workflows/ci.yml' checks minimum NF version
actions_awstest - '.github/workflows/awstest.yml' is triggered correctly
pipeline_name_conventions - Name adheres to nf-core convention
template_strings - Did not find any Jinja template strings (132 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: ci.yml
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: awsfulltest.yml
actions_schema_validation - Workflow validation passed: awstest.yml
actions_schema_validation - Workflow validation passed: linting_comment.yml
actions_schema_validation - Workflow validation passed: branch.yml
merge_markers - No merge markers found in pipeline files

Run details

nf-core/tools version 1.14
Run at 2021-06-07 16:26:02

Correct channel name

antunderwood

@drpatelh

Thanks for all your hard work putting in effort to bringing this up to latest DSL2 standards/conventions. I have just a couple of comments about the usage.md

docs/usage.md

drpatelh added 23 commits May 28, 2021 13:30

Remove changed lib/ files

f085490

Replace lib/ files with latest

87ddb15

Remove comment about software versions

393ac9b

Replace awsfulltest.yml with latest

7478acd

Replace awstest.yml with latest

09f74c1

Bump NF version for CI tests

05bfffc

Copy across latest template updates to README.md

53259ff

Remove unrequired files

6d6249a

Add DSL2 specific docs for changing options

4f4e579

Strip out all biolerplate code from main.nf

b649d52

Remove redundant function in

44b96c4

Change parameter values to null and update profiles in nextflow.config

f1cf53b

Small updates to spacing in subworkflows

0382788

Aesthetic updats

3a45e96

Add pipeline summary to CHANGELOG

de2067f

Add in missing header

8194003

Use latest functions.nf

b2e6c5a

Remove igenomes.config

ef25e52

Replace info section in modules.config

fb97f8d

Adjust spacing in test.config

60dda2e

Adjust spacing in test_full.config

a2c923c

Comment out comment in bactmap.nf

8b7484b

Fix nf-core lint

d49db0a

drpatelh mentioned this pull request May 28, 2021

Pseudo PR - DO NOT MERGE #29

Closed

drpatelh added 2 commits June 1, 2021 09:21

Fix comment style across all nf files

c85b2ae

Change location of .markdownlint.yml and add 4 indent style

a4c34df

drpatelh changed the title ~~Pre-release fixes and partial syncing with latest DSL2 pipeline template~~ Pre-release fixes and syncing with latest DSL2 pipeline template Jun 1, 2021

drpatelh added 2 commits June 1, 2021 09:28

Fix markdownlint

81fc774

Add EditorConfig CI tests

075f795

drpatelh and others added 6 commits June 1, 2021 09:32

Try to fix nf-core linting

f37be3e

First pass ECLint fixes

8681f16

Final EClint fixes

9dea3b9

Fix nf-core lint

75b2337

Remove TODO statement from awsfulltest.yml

6818049

Update bactmap.nf

70e2b79

Correct channel name

antunderwood reviewed Jun 3, 2021

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antunderwood added 3 commits June 7, 2021 17:20

Pull out resource usage and module configuration into separate docs

2299630

Merge branch 'fixes' of https://github.com/drpatelh/bactmap into fixes

860f0f5

Fix linting issues

bad6c78

antunderwood approved these changes Jun 7, 2021

View reviewed changes

antunderwood merged commit 8bbe33e into nf-core:dev Jun 7, 2021

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Pre-release fixes and syncing with latest DSL2 pipeline template #38

Pre-release fixes and syncing with latest DSL2 pipeline template #38

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drpatelh commented May 28, 2021

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github-actions bot commented May 28, 2021 •

edited

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❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

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Pre-release fixes and syncing with latest DSL2 pipeline template #38

Pre-release fixes and syncing with latest DSL2 pipeline template #38

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drpatelh commented May 28, 2021

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nf-core lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

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github-actions bot commented May 28, 2021 •

edited

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