nf-core modules update all with prefix annotation by FriederikeHanssen · Pull Request #462 · nf-core/sarek

FriederikeHanssen · 2021-12-06T10:02:09Z

PR checklist

maxulysse

ok for me even if the nf-core lint is not working.
It's made with dev, so I expect it not to be working all the time, I'll make a separate PR to fix the dark/light mode of the logos

… vairable task'

github-actions · 2021-12-07T09:37:31Z

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

Posted for pipeline commit 5061cbc

+| ✅ 135 tests passed       |+
#| ❔   6 tests were ignored |#
!| ❗   5 tests had warnings |!

Details

❗ Test warnings:

pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
pipeline_todos - TODO string in test_full.config: Specify the paths to your full test data ( on nf-core/test-datasets or directly in repositories, e.g. SRA)
pipeline_todos - TODO string in test_full.config: Give any required params for the test so that command line flags are not needed
pipeline_todos - TODO string in test_full.config: Specify the paths to your full test data ( on nf-core/test-datasets or directly in repositories, e.g. SRA)
pipeline_todos - TODO string in test_full.config: Give any required params for the test so that command line flags are not needed

❔ Tests ignored:

files_unchanged - File ignored due to lint config: .github/workflows/linting.yml
files_unchanged - File ignored due to lint config: assets/nf-core-sarek_logo_light.png
files_unchanged - File ignored due to lint config: docs/images/nf-core-sarek_logo_light.png
files_unchanged - File ignored due to lint config: docs/images/nf-core-sarek_logo_dark.png
files_unchanged - File ignored due to lint config: lib/NfcoreTemplate.groovy
files_unchanged - File ignored due to lint config: assets/multiqc_config.yaml

✅ Tests passed:

files_exist - File found: .gitattributes
files_exist - File found: .gitignore
files_exist - File found: .markdownlint.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-sarek_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-sarek_logo_light.png
files_exist - File found: docs/images/nf-core-sarek_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.yaml
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/WorkflowSarek.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: 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-sarek_logo.png
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: '3.0dev'
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 - .markdownlint.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 - 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 - 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
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 badge matched config. Badge: 21.10.3, Config: 21.10.3
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 (249 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: awsfulltest.yml
actions_schema_validation - Workflow validation passed: branch.yml
actions_schema_validation - Workflow validation passed: ci.yml
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: awstest.yml
actions_schema_validation - Workflow validation passed: local_modules.yml
actions_schema_validation - Workflow validation passed: linting_comment.yml
merge_markers - No merge markers found in pipeline files
modules_json - Only installed modules found in modules.json

Run details

nf-core/tools version 2.2.dev0
Run at 2021-12-08 19:44:35

maxulysse · 2021-12-07T15:01:14Z

🚀

…quired

FriederikeHanssen · 2021-12-08T20:28:21Z

@maxulysse I think I would leave it as is now and add the mapping workflow together with the UMI sub workflow. The gatk4 modules need upstream updates as discussed, so would also push it to the next PR to allow others to use the updated syntax now

FriederikeHanssen added 8 commits December 6, 2021 11:01

nf-core modules update all

5f66efd

replace suffix for nf-core modules with prefix

1b0632e

one ci test at a time

c88c0b6

one ci test at a time

ab931d8

one ci test at a time, tmor normal pair passes locally but not here

cea0e31

one ci test at a time, tmor normal pair passes locally but not here

998e80d

one ci test at a time

cbce8e4

one ci test at a time

da2e677

maxulysse approved these changes Dec 6, 2021

View reviewed changes

FriederikeHanssen added 2 commits December 6, 2021 12:43

one ci test at a time, annotation wf not passing, some issue with 'no…

949acfe

… vairable task'

Update modules again

941d089

maxulysse reviewed Dec 6, 2021

View reviewed changes

Comment thread subworkflows/local/build_indices.nf Outdated

FriederikeHanssen added 2 commits December 6, 2021 13:08

Add meta field because updated samtools faidx modules

aec7bcf

Fix samtools input + channel magic instead of module changes

a0b7a24

maxulysse reviewed Dec 6, 2021

View reviewed changes

Comment thread modules/local/build_intervals/main.nf Outdated

maxulysse reviewed Dec 6, 2021

View reviewed changes

Comment thread subworkflows/local/prepare_genome.nf

Revert changes to build_intervals module

8bc2837

maxulysse reviewed Dec 6, 2021

View reviewed changes

Comment thread subworkflows/local/prepare_genome.nf Outdated

Add name to samtools faidx call & turn off annotation sw for debugging

9008a5f

maxulysse mentioned this pull request Dec 6, 2021

Update modules once again #459

Merged

11 tasks

FriederikeHanssen added 7 commits December 6, 2021 21:31

Fix annotation subworkflow

269b37f

Move 'parts' logic to config

117f152

apprantly splitfastq test got overwritten at som epoint

2b6b512

🤦 update ci file

5a5bdda

Add yml for testing, edit config to latest nf release

18c26c0

Remove local tabix module, update tabix & seqkit

903f388

Update snpeff & vep

be6397b

FriederikeHanssen added 2 commits December 7, 2021 10:39

use correct path for including tabix modules

976625f

Removing parts from bwa mem, splot tests not working 😢

7708266

maxulysse reviewed Dec 7, 2021

View reviewed changes

Comment thread conf/modules.config Outdated

maxulysse reviewed Dec 7, 2021

View reviewed changes

Comment thread conf/modules.config Outdated

FriederikeHanssen added 2 commits December 7, 2021 15:11

apply code review

9850be7

fix split tests (hopefully), test separatly

a1ff42d

FriederikeHanssen added 8 commits December 7, 2021 17:01

add tests back in (except annotation, because it fails)

48dc9d8

add tests back in (except annotation, because it fails)

915ade2

annotation wf runs locally

06732dc

install gatk4 modules

d7eceae

add nf-core gatk4 modules in another PR as some upstream fixes are re…

ba78251

…quired

replace VEP sw with nf-core/vep sw

fc89462

add snpeff sw and properly import it

06d100b

update config with changed module and sw names

5061cbc

FriederikeHanssen marked this pull request as ready for review December 8, 2021 20:27

FriederikeHanssen requested a review from maxulysse December 8, 2021 20:28

maxulysse merged commit 9094f13 into nf-core:dev Dec 8, 2021

maxulysse mentioned this pull request Dec 8, 2021

Remove local + update modules + nf-corize mapping subworkflow #466

Merged

11 tasks

FriederikeHanssen deleted the update_modules branch July 10, 2023 18:59

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nf-core modules update all with prefix annotation#462

nf-core modules update all with prefix annotation#462
maxulysse merged 33 commits intonf-core:devfrom
FriederikeHanssen:update_modules

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github-actions Bot commented Dec 7, 2021 •

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❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

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maxulysse commented Dec 7, 2021

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FriederikeHanssen commented Dec 8, 2021

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FriederikeHanssen commented Dec 6, 2021

PR checklist

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github-actions Bot commented Dec 7, 2021 • edited Loading Uh oh! There was an error while loading. Please reload this page.

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nf-core lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

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maxulysse commented Dec 7, 2021

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FriederikeHanssen commented Dec 8, 2021

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github-actions Bot commented Dec 7, 2021 •

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