Immcantation devel #259

ggabernet · 2023-05-24T18:31:50Z

Not to be merged until next EnchantR release is out

PR checklist

This comment contains a description of changes (with reason).
If you've fixed a bug or added code that should be tested, add tests!
If you've added a new tool - have you followed the pipeline conventions in the contribution docs- [ ] If necessary, also make a PR on the nf-core/airrflow branch on the nf-core/test-datasets repository.
Make sure your code lints (nf-core lint).
Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
Usage Documentation in docs/usage.md is updated.
Output Documentation in docs/output.md is updated.
CHANGELOG.md is updated.
README.md is updated (including new tool citations and authors/contributors).

dowser updates

github-actions · 2023-05-24T18:36:02Z

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

Posted for pipeline commit 9ec2002

+| ✅ 159 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 prefered 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
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-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
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: .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: .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.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.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/
nextflow_config - Config dag.file ended with .html
nextflow_config - Config variable manifest.nextflowVersion started with >= or !>=
nextflow_config - Config manifest.version ends in dev: '3.2.0dev'
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 - .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/NfcoreSchema.groovy 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: 22.10.1, Config: 22.10.1
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 (162 files)
schema_lint - Schema lint passed
schema_lint - Schema title + description lint passed
schema_lint - Input mimetype lint passed: 'text/tsv'
schema_params - Schema matched params returned from nextflow config
system_exit - No System.exit calls found
actions_schema_validation - Workflow validation passed: clean-up.yml
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: branch.yml
actions_schema_validation - Workflow validation passed: ci_immcantation.yml
actions_schema_validation - Workflow validation passed: awsfulltest.yml
actions_schema_validation - Workflow validation passed: fix-linting.yml
actions_schema_validation - Workflow validation passed: awstest.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'.
modules_structure - modules directory structure is correct 'modules/nf-core/TOOL/SUBTOOL'

Run details

nf-core/tools version 2.8
Run at 2023-06-23 14:53:35

3.1.0 release: Template update and minor bugfixes

Update immcantation-devel changes

into parametrize-findthreshold

Parametrize findthreshold

into immcantation-devel

Update EnchantR to 0.1.3

assets/repertoire_comparison.Rmd

ssnn-airr and others added 8 commits March 21, 2023 18:46

fixed typo in docs

3871d43

dont write filter pass output repertoire if empty

323bb6f

forgot to make this output optional

55f002f

added dowser ext.args minseq, traits and tips

57a6ec4

Merge branch 'dev' of https://github.com/nf-core/airrflow into dev

29f0618

Merge branch 'dev' of https://github.com/nf-core/airrflow into dev

9f065ed

updated error message

67ffd27

Merge pull request #254 from immcantation/dev

06d69c1

dowser updates

ggabernet added the do not merge label May 24, 2023

ggabernet changed the base branch from master to dev May 24, 2023 20:31

nf-core deleted a comment from github-actions bot May 24, 2023

ssnn-airr and others added 18 commits May 27, 2023 10:28

rm to have igblast reassign the c_call

a1e4674

Merge branch 'dev' of https://github.com/nf-core/airrflow into dev

b969a7a

Merge branch 'dev' of https://github.com/nf-core/airrflow into dev

25b3abe

Merge branch 'dev' of https://github.com/nf-core/airrflow into dev

ada49d0

Merge branch 'dev' of https://github.com/nf-core/airrflow into dev

bfb1de0

Merge pull request #262 from nf-core/dev

a2a6099

3.1.0 release: Template update and minor bugfixes

Merge branch 'dev' of https://github.com/nf-core/airrflow into dev

744894c

fix error directory or other parameter too long

4808422

revert

92988fa

(＠_＠)

2cd8a53

fixes for large .command.sh

d669012

fixes for large .commad.sh

48d8826

user airr, stringi and subset data

a644882

fix report use read rearrangement

be281bd

add samplesheet check assembled

716fc5e

fix black linting

b6c89e9

back to dev version

db67677

fix var name

c42be4f

ggabernet and others added 19 commits June 20, 2023 16:07

Update assets/repertoire_comparison.Rmd

39f34a5

Update assets/repertoire_comparison.Rmd

9490ce0

Add params findthreshold

402cb7f

update changelog

b53a6a1

species mix not allowed use a samplesheet per species

f0862bc

updated confis and tests to use separate hs and mm

fb228de

Merge branch 'dev' of github.com:immcantation/bcellmagic into dev

993680e

enable convergence define clones report

359c4b1

Merge branch 'nf-core:immcantation-devel' into immcantation-devel

058f6f9

Merge pull request #260 from immcantation/dev

7518036

Update immcantation-devel changes

Merge branch 'immcantation-devel' of https://github.com/nf-core/airrflow

33dbea5

into parametrize-findthreshold

allow for locus lowercase

56e4c86

fix linting

dfaff52

update changelog

074c4f5

fix linting

9bcef93

Merge pull request #268 from ggabernet/parametrize-findthreshold

e22c277

Parametrize findthreshold

Merge branch 'immcantation-devel' of https://github.com/nf-core/airrflow

9bd04ac

into immcantation-devel

update to enchantr 0.1.3

e747884

update changelog

9746d8e

ggabernet requested a review from ssnn-airr June 23, 2023 13:31

ggabernet marked this pull request as ready for review June 23, 2023 13:31

Merge pull request #269 from ggabernet/immcantation-devel

9cce811

Update EnchantR to 0.1.3

ggabernet added ready for review and merge and removed do not merge labels Jun 23, 2023

ggabernet commented Jun 23, 2023

View reviewed changes

assets/repertoire_comparison.Rmd Outdated Show resolved Hide resolved

Update assets/repertoire_comparison.Rmd

9ec2002

ssnn-airr approved these changes Jun 30, 2023

View reviewed changes

ggabernet merged commit 06ab934 into dev Jul 1, 2023

ggabernet deleted the immcantation-devel branch August 15, 2023 20:33

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Immcantation devel #259

Immcantation devel #259

ggabernet commented May 24, 2023 •

edited

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github-actions bot commented May 24, 2023 •

edited

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❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

Immcantation devel #259

Immcantation devel #259

Conversation

ggabernet commented May 24, 2023 • edited Loading

Not to be merged until next EnchantR release is out

PR checklist

github-actions bot commented May 24, 2023 • edited Loading

nf-core lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

ggabernet commented May 24, 2023 •

edited

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github-actions bot commented May 24, 2023 •

edited

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