First release PR #4

FriederikeHanssen · 2024-03-01T12:55:22Z

Tested on two cancer studies on the CFC in addition to the CI tests

Merge in the several template updates
Update modules

PR checklist

Small steps - First working version

Template 2.13.1

github-actions · 2024-03-12T15:29:45Z

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

Posted for pipeline commit 16e0135

+| ✅ 138 tests passed       |+
#| ❔  21 tests were ignored |#
!| ❗   7 tests had warnings |!

❗ Test warnings:

nextflow_config - Config manifest.version should end in dev: 1.0.0
readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
pipeline_todos - TODO string in README.md: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file.
pipeline_todos - TODO string in README.md: Add bibliography of tools and data used in your pipeline
pipeline_todos - TODO string in main.nf: Optionally add in-text citation tools to this list.
pipeline_todos - TODO string in main.nf: Optionally add bibliographic entries to this list.
pipeline_todos - TODO string in main.nf: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!

❔ Tests ignored:

files_exist - File is ignored: CODE_OF_CONDUCT.md
files_exist - File is ignored: assets/nf-core-vcftomaf_logo_light.png
files_exist - File is ignored: docs/images/nf-core-vcftomaf_logo_light.png
files_exist - File is ignored: docs/images/nf-core-vcftomaf_logo_dark.png
files_exist - File is ignored: .github/ISSUE_TEMPLATE/config.yml
files_exist - File is ignored: .github/workflows/awstest.yml
files_exist - File is ignored: .github/workflows/awsfulltest.yml
files_exist - File is ignored: conf/test_full.config
nextflow_config - Config variable ignored: manifest.name
nextflow_config - Config variable ignored: manifest.homePage
files_unchanged - File ignored due to lint config: CODE_OF_CONDUCT.md
files_unchanged - File ignored due to lint config: .github/CONTRIBUTING.md
files_unchanged - File ignored due to lint config: .github/ISSUE_TEMPLATE/bug_report.yml
files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
files_unchanged - File ignored due to lint config: assets/email_template.txt
files_unchanged - File ignored due to lint config: assets/sendmail_template.txt
files_unchanged - File ignored due to lint config: assets/nf-core-vcftomaf_logo_light.png
files_unchanged - File ignored due to lint config: docs/images/nf-core-vcftomaf_logo_light.png
files_unchanged - File ignored due to lint config: docs/images/nf-core-vcftomaf_logo_dark.png
files_unchanged - File ignored due to lint config: docs/README.md
actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/vcftomaf/vcftomaf/.github/workflows/awstest.yml

✅ 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: .prettierignore
files_exist - File found: .prettierrc.yml
files_exist - File found: CHANGELOG.md
files_exist - File found: CITATIONS.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/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: conf/modules.config
files_exist - File found: conf/test.config
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: 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: modules.json
files_exist - File found: pyproject.toml
files_exist - File not found check: Singularity
files_exist - File not found check: parameters.settings.json
files_exist - File not found check: pipeline_template.yml
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-vcftomaf_logo.png
files_exist - File not found check: .markdownlint.yml
files_exist - File not found check: .yamllint.yml
files_exist - File not found check: lib/Checks.groovy
files_exist - File not found check: lib/Completion.groovy
files_exist - File not found check: lib/Workflow.groovy
files_exist - File not found check: lib/Utils.groovy
files_exist - File not found check: lib/WorkflowMain.groovy
files_exist - File not found check: lib/NfcoreTemplate.groovy
files_exist - File not found check: lib/WorkflowVcftomaf.groovy
files_exist - File not found check: lib/nfcore_external_java_deps.jar
files_exist - File not found check: .travis.yml
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: 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.validationShowHiddenParams
nextflow_config - Config variable found: params.validationSchemaIgnoreParams
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.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 variable (correctly) not found: params.enable_conda
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 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
nextflow_config - nextflow.config contains configuration profile test
nextflow_config - Config default value correct: params.igenomes_base= s3://ngi-igenomes/igenomes
nextflow_config - Config default value correct: params.custom_config_version= master
nextflow_config - Config default value correct: params.custom_config_base= https://raw.githubusercontent.com/nf-core/configs/master
nextflow_config - Config default value correct: params.max_cpus= 16
nextflow_config - Config default value correct: params.max_memory= 128.GB
nextflow_config - Config default value correct: params.max_time= 240.h
nextflow_config - Config default value correct: params.publish_dir_mode= copy
nextflow_config - Config default value correct: params.max_multiqc_email_size= 25.MB
nextflow_config - Config default value correct: params.validate_params= true
files_unchanged - .gitattributes matches the template
files_unchanged - .prettierrc.yml matches the template
files_unchanged - LICENSE matches the template
files_unchanged - .github/.dockstore.yml matches the template
files_unchanged - .github/ISSUE_TEMPLATE/feature_request.yml 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 - .gitignore matches the template
files_unchanged - .prettierignore matches the template
files_unchanged - pyproject.toml matches the template
actions_ci - '.github/workflows/ci.yml' is triggered on expected events
actions_ci - '.github/workflows/ci.yml' checks minimum NF version
readme - README Nextflow minimum version badge matched config. Badge: 23.04.0, Config: 23.04.0
pipeline_name_conventions - Name adheres to nf-core convention
template_strings - Did not find any Jinja template strings (130 files)
schema_lint - Schema lint passed
schema_lint - Schema title + description lint passed
schema_lint - Input mimetype lint passed: 'text/csv'
schema_params - Schema matched params returned from nextflow config
system_exit - No System.exit calls found
actions_schema_validation - Workflow validation passed: branch.yml
actions_schema_validation - Workflow validation passed: download_pipeline.yml
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: linting_comment.yml
actions_schema_validation - Workflow validation passed: clean-up.yml
actions_schema_validation - Workflow validation passed: ci.yml
actions_schema_validation - Workflow validation passed: fix-linting.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' contains report_section_order
multiqc_config - 'assets/multiqc_config.yml' contains export_plots
multiqc_config - 'assets/multiqc_config.yml' contains report_comment
multiqc_config - 'assets/multiqc_config.yml' follows the ordering scheme of the minimally required plugins.
multiqc_config - 'assets/multiqc_config.yml' contains 'export_plots: true'.
modules_structure - modules directory structure is correct 'modules/nf-core/TOOL/SUBTOOL'

Run details

nf-core/tools version 2.13.1
Run at 2024-03-13 09:36:26

Dockerfile

conf/test_vep.config

Disable VEP

mirpedrol

LGTM! Only some small suggestions :)

.github/PULL_REQUEST_TEMPLATE.md

.github/workflows/ci.yml

CHANGELOG.md

README.md

nextflow.config

docs/usage.md

workflows/vcftomaf.nf

main.nf

adress reviews

FriederikeHanssen · 2024-03-13T09:37:02Z

I am going with extended colors and baby animals for release names for this pipeline. How about: Plum Puppy

mirpedrol · 2024-03-13T09:40:59Z

I am going with extended colors and baby animals for release names for this pipeline. How about: Plum Puppy

It matches with nf-core/tools 2.13 Tin Puppy 😄

SusiJo and others added 30 commits August 3, 2023 08:37

ch to qbic-pipelines

b8835fe

first working version

6c6eed2

testing successful

8d54af3

docu

550c3eb

add docu

7803ef9

prettier + paths

56d3218

add test.config

687dc9f

add ci + rm todo

dac80f8

ignore files

6228c3b

add to changelog

7b1ac4b

rm fastq module + add unique key

e3527d8

apply suggestions from code review

77638ac

update ensembl-vep

51a9ce3

add container for umccr/vcf2maf

871175b

apply review suggestions

f6c0a7d

add qbic-logo images

33184ec

add qbic info

ee86767

add mulled container bioconda

4f24be2

ch channel to bioconda

8a5c18e

Merge pull request #1 from SusiJo/first_version

93049d5

Small steps - First working version

remove unused module, attempt to fix id mess for maf ids

0c00d07

add closure

e4862f9

fix vcf id

7aa3604

remove view statement

897cdd4

fix config

27039e3

add picard liftover

6b65e35

fix naming

4a7ea8b

add view statements for debugging

415190f

Initialise dict

28ad1d3

fix initialising

f023b11

FriederikeHanssen added 18 commits March 12, 2024 12:04

debug weird function error

0514c29

debug weird function error

b5de7f7

debug weird function error

a3d72a3

debug weird function error

162ec90

maybe the schema is the cuprit

b9d2c23

maybe the schema is the cuprit

fe589f2

maybe the schema is the cuprit

020e1ba

why

f6465a2

why

6c17d18

why

3b1c35f

why

d89bb87

why

84ac478

why

a41d0d4

why

48b9f86

why

848fa2d

why

62aca73

chain is a reserved word

36c9960

Merge pull request #6 from FriederikeHanssen/template

591f1a9

Template 2.13.1

FriederikeHanssen commented Mar 12, 2024

View reviewed changes

Dockerfile Outdated Show resolved Hide resolved

FriederikeHanssen commented Mar 12, 2024

View reviewed changes

conf/test_vep.config Outdated Show resolved Hide resolved

FriederikeHanssen added 3 commits March 12, 2024 16:33

Apply suggestions from code review

e3dea66

remove VEP

1ab53dc

Merge pull request #7 from FriederikeHanssen/disabe_vep

6bcc689

Disable VEP

mirpedrol approved these changes Mar 13, 2024

View reviewed changes

FriederikeHanssen added 2 commits March 13, 2024 09:26

adress reviews

5080acf

Merge pull request #8 from FriederikeHanssen/reviewcomments

16e0135

adress reviews

FriederikeHanssen merged commit 3830fb5 into master Mar 13, 2024
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First release PR #4

First release PR #4

FriederikeHanssen commented Mar 1, 2024 •

edited

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github-actions bot commented Mar 12, 2024 •

edited

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❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

mirpedrol left a comment

FriederikeHanssen commented Mar 13, 2024

mirpedrol commented Mar 13, 2024

First release PR #4

First release PR #4

Conversation

FriederikeHanssen commented Mar 1, 2024 • edited Loading

PR checklist

github-actions bot commented Mar 12, 2024 • edited Loading

nf-core lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

mirpedrol left a comment

Choose a reason for hiding this comment

FriederikeHanssen commented Mar 13, 2024

mirpedrol commented Mar 13, 2024

FriederikeHanssen commented Mar 1, 2024 •

edited

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github-actions bot commented Mar 12, 2024 •

edited

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