PSEUDO PR - DO NOT MERGE #2

ewels · 2022-06-17T07:28:16Z

PSEUDO PR - DO NOT MERGE

This is the pseudo-PR that we use for the community review leading up to the first release of this nf-core pipeline.

Please do not merge the PR, as that closes it and all associated discussion. However, you can use the GitHub reviewing interface to add reviews and inline comments to the code.

To do before first release

At least one more review from someone else, preferably two
Check documentation is up to date and complete
Test running the pipeline offline
Remove nf-core lint warnings if possible

Update Markdown

All Markdown files containing information about the pipeline need to be up to date including output.md, usage.md and README.md.

README.md
output.md
usage.md
nextflow_schema.json (documentation via nf-core schema build)

Minor updates on comments

github-actions · 2022-06-17T07:29:29Z

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

Posted for pipeline commit 29e6cbc

+| ✅ 146 tests passed       |+
!| ❗   3 tests had warnings |!

❗ Test warnings:

nextflow_config - Config manifest.version should end in dev: '1.0.0'
readme - README did not have a Nextflow minimum version badge.
pipeline_todos - TODO string in WorkflowMain.groovy: Add Zenodo DOI for pipeline after first release

✅ Tests passed:

files_exist - File found: .gitattributes
files_exist - File found: .gitignore
files_exist - File found: .nf-core.yml
files_exist - File found: .editorconfig
files_exist - File found: .prettierrc.yml
files_exist - File found: CHANGELOG.md
files_exist - File found: CITATIONS.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.yml
files_exist - File found: .github/ISSUE_TEMPLATE/config.yml
files_exist - File found: .github/ISSUE_TEMPLATE/feature_request.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-isoseq_logo_light.png
files_exist - File found: conf/modules.config
files_exist - File found: conf/test.config
files_exist - File found: conf/test_full.config
files_exist - File found: docs/images/nf-core-isoseq_logo_light.png
files_exist - File found: docs/images/nf-core-isoseq_logo_dark.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: lib/NfcoreTemplate.groovy
files_exist - File found: lib/Utils.groovy
files_exist - File found: lib/WorkflowMain.groovy
files_exist - File found: main.nf
files_exist - File found: assets/multiqc_config.yml
files_exist - File found: conf/base.config
files_exist - File found: conf/igenomes.config
files_exist - File found: .github/workflows/awstest.yml
files_exist - File found: .github/workflows/awsfulltest.yml
files_exist - File found: lib/WorkflowIsoseq.groovy
files_exist - File found: modules.json
files_exist - File not found check: Singularity
files_exist - File not found check: parameters.settings.json
files_exist - File not found check: .nf-core.yaml
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: .github/ISSUE_TEMPLATE/bug_report.md
files_exist - File not found check: .github/ISSUE_TEMPLATE/feature_request.md
files_exist - File not found check: docs/images/nf-core-isoseq_logo.png
files_exist - File not found check: .markdownlint.yml
files_exist - File not found check: .yamllint.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 .html
nextflow_config - Config variable manifest.nextflowVersion started with >= or !>=
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 - .prettierrc.yml 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.yml matches the template
files_unchanged - .github/ISSUE_TEMPLATE/config.yml matches the template
files_unchanged - .github/ISSUE_TEMPLATE/feature_request.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-isoseq_logo_light.png matches the template
files_unchanged - docs/images/nf-core-isoseq_logo_light.png matches the template
files_unchanged - docs/images/nf-core-isoseq_logo_dark.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 - lib/NfcoreTemplate.groovy matches the template
files_unchanged - .gitignore 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
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 in Quick Start section matched config. README: 21.10.3, Config: 21.10.3
pipeline_name_conventions - Name adheres to nf-core convention
template_strings - Did not find any Jinja template strings (97 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: awstest.yml
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: awsfulltest.yml
actions_schema_validation - Workflow validation passed: branch.yml
actions_schema_validation - Workflow validation passed: fix-linting.yml
actions_schema_validation - Workflow validation passed: linting_comment.yml
actions_schema_validation - Workflow validation passed: ci.yml
merge_markers - No merge markers found in pipeline files
modules_json - Only installed modules found in modules.json
multiqc_config - 'assets/multiqc_config.yml' follows the ordering scheme of the minimally required plugins.
multiqc_config - 'assets/multiqc_config.yml' contains a matching 'report_comment'.
multiqc_config - 'assets/multiqc_config.yml' contains 'export_plots: true'.

Run details

nf-core/tools version 2.4.1
Run at 2022-06-20 11:24:11

JoseEspinosa

Awesome job @sguizard! 🚀
I just dropped some suggestions but otherwise looks almost ready for release. It might be worth thought that someone familiar with isoseq analysis might take a look too.

CITATIONS.md

README.md

conf/base.config

modules/local/gstama/filelist/main.nf

modules/nf-core/modules/bamtools/convert/main.nf

nextflow.config

nextflow_schema.json

workflows/isoseq.nf

Co-authored-by: Jose Espinosa-Carrasco <[email protected]>

Remove stageInMode

Replace biocontainers/biocontainers:v1.2.0_cv1 by ubuntu:20.04

Correct publish mode setup

Set default to null

Reintegrate CUSTOM_DUMPSOFTWAREVERSIONS

uncomment SAMPLESHEET_CHECK and CUSTOM_DUMPSOFTWAREVERSIONS configs

Co-authored-by: Jose Espinosa-Carrasco <[email protected]>

sguizard · 2022-06-20T07:54:19Z

@JoseEspinosa I applied your corrections/suggestions.
Can you give assistance to clean the test-datasets master branch? I first pushed the data on it 😅

JoseEspinosa

Thanks a lot @sguizard 🚀

CITATIONS.md

JoseEspinosa · 2022-06-20T08:05:43Z

@JoseEspinosa I applied your corrections/suggestions. Can you give assistance to clean the test-datasets master branch? I first pushed the data on it 😅

Sure, you just need to create a PR to the master branch in which you remove the files you included there, ping me and I can review it.

DSchreyer

The pipeline is in a good state for publication. I just had some minor comments, which can be resolved easily. The pipeline works as expected and the documentation is almost complete. Imo it is ready for the official review.

bin/check_samplesheet.py

nextflow_schema.json

sguizard · 2022-06-20T10:35:03Z

@JoseEspinosa @DSchreyer I finished making corrections, Thanks for your reviews!
What is the next step now?

DSchreyer · 2022-06-20T10:47:55Z

@JoseEspinosa @DSchreyer I finished making corrections, Thanks for your reviews! What is the next step now?

sguizard · 2022-06-20T10:48:56Z

Update of MultiQC broke the pipeline, let me fix this please

DSchreyer · 2022-06-20T10:50:05Z

e, let me fix this please

Yes, sorry. closing issue was unintentionally. Could you also address the last review of the css parameters in the nextflow_schema.json file. Then you are good to go!

sguizard · 2022-06-20T11:23:31Z

All Fixed!

DSchreyer · 2022-06-20T12:13:48Z

Well done @sguizard ! Nothing to add !

JoseEspinosa · 2022-06-20T15:25:41Z

@JoseEspinosa @DSchreyer I finished making corrections, Thanks for your reviews! What is the next step now?
Sorry for the late reply. Now you can go for your first release 🚀 See here. There is a release checklist on this link and if you have any doubts just drop them on slack.

sguizard added 3 commits June 3, 2022 10:20

Restart from a clean and fresh project

453ac83

Minor updates on comments

3f3bc2c

Merge pull request #1 from sguizard/dev

b6fef64

Minor updates on comments

ewels added the WIP Work in progress label Jun 17, 2022

JoseEspinosa requested changes Jun 17, 2022

View reviewed changes

sguizard and others added 15 commits June 17, 2022 09:45

Update CITATIONS.md

d94e0dc

Co-authored-by: Jose Espinosa-Carrasco <[email protected]>

Update README.md

b0b8181

Co-authored-by: Jose Espinosa-Carrasco <[email protected]>

Update README.md

f877eba

Co-authored-by: Jose Espinosa-Carrasco <[email protected]>

Update docs/usage.md

717b5c4

Co-authored-by: Jose Espinosa-Carrasco <[email protected]>

Update nextflow_schema.json

a95fd1c

Co-authored-by: Jose Espinosa-Carrasco <[email protected]>

Update base.config

748476f

Remove stageInMode

Update gstama/filelist/main.nf

0c123c7

Replace biocontainers/biocontainers:v1.2.0_cv1 by ubuntu:20.04

Update modules.conf

f687edc

Correct publish mode setup

Update nextflow.config

acf1d5a

Set default to null

Update isoseq.nf

5b4e32a

Reintegrate CUSTOM_DUMPSOFTWAREVERSIONS

Update bamtool/convert

72e35c3

Fix CUSTOM_DUMPSOFTWAREVERSIONS

604333a

Update modules.config

d9387df

uncomment SAMPLESHEET_CHECK and CUSTOM_DUMPSOFTWAREVERSIONS configs

Update docs/usage.md

b234906

Co-authored-by: Jose Espinosa-Carrasco <[email protected]>

Update test data links (pointing nf-core)

ec1c4d6

JoseEspinosa approved these changes Jun 20, 2022

View reviewed changes

CITATIONS.md Show resolved Hide resolved

DSchreyer reviewed Jun 20, 2022

View reviewed changes

bin/check_samplesheet.py Outdated Show resolved Hide resolved

nextflow_schema.json Show resolved Hide resolved

sguizard added 3 commits June 20, 2022 10:19

Update samplesheet reference

47d8588

Update old description message

0f34ecc

Update README.md

b0fae08

Update MultiQC module

56c1867

sguizard added 2 commits June 20, 2022 11:40

Bump version 1.0.0dev -> 1.0.0

9edb128

Bump version in CHANGELOG.md

15390b7

DSchreyer closed this Jun 20, 2022

DSchreyer reopened this Jun 20, 2022

sguizard added 2 commits June 20, 2022 12:09

Fix channel error caused by MultiQC update

2ba1161

Update CCS options descritptions

29e6cbc

sguizard closed this Jun 20, 2022

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PSEUDO PR - DO NOT MERGE #2

PSEUDO PR - DO NOT MERGE #2

ewels commented Jun 17, 2022

github-actions bot commented Jun 17, 2022 •

edited

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❗ Test warnings:

✅ Tests passed:

Run details

JoseEspinosa left a comment

sguizard commented Jun 20, 2022

JoseEspinosa left a comment

JoseEspinosa commented Jun 20, 2022

DSchreyer left a comment

sguizard commented Jun 20, 2022

DSchreyer commented Jun 20, 2022

sguizard commented Jun 20, 2022

DSchreyer commented Jun 20, 2022

sguizard commented Jun 20, 2022

DSchreyer commented Jun 20, 2022

JoseEspinosa commented Jun 20, 2022

PSEUDO PR - DO NOT MERGE #2

PSEUDO PR - DO NOT MERGE #2

Conversation

ewels commented Jun 17, 2022

PSEUDO PR - DO NOT MERGE

To do before first release

Update Markdown

github-actions bot commented Jun 17, 2022 • edited Loading

nf-core lint overall result: Passed ✅ ⚠️

❗ Test warnings:

✅ Tests passed:

Run details

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sguizard commented Jun 20, 2022

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JoseEspinosa commented Jun 20, 2022

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sguizard commented Jun 20, 2022

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sguizard commented Jun 20, 2022

DSchreyer commented Jun 20, 2022

sguizard commented Jun 20, 2022

DSchreyer commented Jun 20, 2022

JoseEspinosa commented Jun 20, 2022

github-actions bot commented Jun 17, 2022 •

edited

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