Update to Enchantr 0.1.7 #278

ggabernet · 2023-09-01T13:06:02Z

PR checklist

…nto dev

Dev

Short term fix issues Dowser singularity container

github-actions · 2023-09-01T13:07:36Z

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

Posted for pipeline commit 5f98b82

+| ✅ 157 tests passed       |+
#| ❔   1 tests were ignored |#
!| ❗   1 tests had warnings |!

❗ Test warnings:

pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline

❔ Tests ignored:

files_exist - File is ignored: conf/igenomes.config

✅ 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: 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
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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
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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-airrflow_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-airrflow_logo_light.png
files_exist - File found: docs/images/nf-core-airrflow_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
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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
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files_exist - File found: .github/workflows/awstest.yml
files_exist - File found: .github/workflows/awsfulltest.yml
files_exist - File found: lib/WorkflowAirrflow.groovy
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-airrflow_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: .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.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 manifest.name began with nf-core/
nextflow_config - Config variable manifest.homePage began with https://github.com/nf-core/
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nextflow_config - Config variable manifest.nextflowVersion started with >= or !>=
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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-airrflow_logo_light.png matches the template
files_unchanged - docs/images/nf-core-airrflow_logo_light.png matches the template
files_unchanged - docs/images/nf-core-airrflow_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/NfcoreTemplate.groovy 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
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: 23.04.0, Config: 23.04.0
readme - README Zenodo placeholder was replaced with DOI.
pipeline_name_conventions - Name adheres to nf-core convention
template_strings - Did not find any Jinja template strings (163 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: ci.yml
actions_schema_validation - Workflow validation passed: fix-linting.yml
actions_schema_validation - Workflow validation passed: awsfulltest.yml
actions_schema_validation - Workflow validation passed: branch.yml
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: clean-up.yml
actions_schema_validation - Workflow validation passed: awstest.yml
actions_schema_validation - Workflow validation passed: ci_immcantation.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
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 2.10
Run at 2023-10-14 02:00:33

ggabernet · 2023-09-25T14:09:53Z

@nf-core-bot fix linting

…erge-template-updates

merge nf-core tools template update

github-actions · 2023-10-13T01:15:02Z

Python linting (`black`) is failing

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To fix this CI test, please run:

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Fix formatting errors in your pipeline: black .

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nf-core-bot and others added 17 commits June 30, 2023 16:12

Template update for nf-core/tools version 2.9

5d1ea04

allow passing custom fields buildconsensus

623d60e

updated config for threshold report with subsample

e2deaa1

add default params to report threshold

e9b59c6

fix igphyml param docs

5b53226

partial fix for docker container

9a05343

update changelog

6f44bbd

update nextflow config

85d533a

try fix docker singularity issue

9828750

add skip report threshold

f738e5b

fix param skip threshold

a05bcff

add immcantation container for dowser

9a00f03

Merge branch 'dev' of https://github.com/ggabernet/nf-core-airrflow i…

ba97eb3

…nto dev

updated path for enchantr 0.1.4

feedb3f

Merge branch 'dev' into dev

6e9a890

Merge pull request #69 from immcantation/dev

ab6419d

Dev

Merge pull request #276 from ggabernet/dev

f901c87

Short term fix issues Dowser singularity container

ggabernet added 3 commits September 18, 2023 18:00

test immcantation suite prerelease

33da6e5

update path igphyml

216706e

change dowser lineages container

0b44403

nf-core-bot and others added 8 commits September 25, 2023 14:10

[automated] Fix linting with Prettier

58792ce

fix editorconfig linting

db93f27

Merge branch 'TEMPLATE' of https://github.com/nf-core/airrflow into m…

da0c048

…erge-template-updates

add input schema

710accc

fix samplesheet validation

78072bd

update nextflow ver

6db55b0

fix nextflow badge

56756a2

fix lint errors

61b3403

ggabernet and others added 10 commits September 25, 2023 16:25

update to immcantation/airrflow container

c9321ee

update changelog

41f5e12

fix linting errors nf-core v2.10

5a2f42d

Merge pull request #279 from ggabernet/merge-template-updates

1c6816c

merge nf-core tools template update

temporary inactivate validate params

14f2c80

dowser clones by cloneby

e762a6a

findthreshold optional output

c20157a

report clones by cloneby

da21e20

fix tcr tests

ad4eac6

allow whitespace in tissue

5358d66

ggabernet changed the title ~~Enchantr 0.1.5~~ Update to Enchantr 0.1.7 Oct 13, 2023

fix lint

5f98b82

ggabernet marked this pull request as ready for review October 14, 2023 01:59

ssnn-airr approved these changes Oct 15, 2023

View reviewed changes

ggabernet merged commit 9743661 into dev Oct 16, 2023
24 checks passed

ggabernet deleted the enchantr-0.1.5 branch October 23, 2023 15:37

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Update to Enchantr 0.1.7 #278

Update to Enchantr 0.1.7 #278

ggabernet commented Sep 1, 2023

github-actions bot commented Sep 1, 2023 •

edited

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❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

ggabernet commented Sep 25, 2023

github-actions bot commented Oct 13, 2023

Update to Enchantr 0.1.7 #278

Update to Enchantr 0.1.7 #278

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ggabernet commented Sep 1, 2023

PR checklist

github-actions bot commented Sep 1, 2023 • edited Loading

nf-core lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

ggabernet commented Sep 25, 2023

github-actions bot commented Oct 13, 2023

Python linting (black) is failing

github-actions bot commented Sep 1, 2023 •

edited

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

Python linting (`black`) is failing