Update immcantation-devel changes #260

ggabernet · 2023-05-29T17:25:22Z

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).

…-fix

…rflow into report-fix

Report fix and other bugfixes

github-actions · 2023-05-29T17:27:04Z

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

Posted for pipeline commit 993680e

+| ✅ 158 tests passed       |+
#| ❔   1 tests were ignored |#
!| ❗   2 tests had warnings |!

❗ Test warnings:

nextflow_config - Config manifest.version should end in dev: '3.1.0'
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 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: 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: awsfulltest.yml
actions_schema_validation - Workflow validation passed: ci_immcantation.yml
actions_schema_validation - Workflow validation passed: fix-linting.yml
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: awstest.yml
actions_schema_validation - Workflow validation passed: branch.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 2023-06-21 14:44:40

bump versions to 3.1.0

Co-authored-by: Maxime U Garcia <[email protected]>

Apply review corrections and tool version update

assets/repertoire_comparison.Rmd

ggabernet · 2023-06-22T17:51:54Z

@nf-core-bot fix linting

assets/repertoire_comparison.Rmd

conf/test_assembled_mm.config

ssnn-airr · 2023-06-22T18:02:17Z

modules/local/changeo/changeo_parsedb_select.nf

@@ -22,7 +22,7 @@ process CHANGEO_PARSEDB_SELECT {
    def args2 = task.ext.args2 ?: ''
    if (meta.locus == 'IG'){


Is this case sensitive? Could it happen that locus is lower case, and then we should check 'IG' and 'ig'?

I will correct it in the follow-up PR where there is also a change related to this, thanks!

ggabernet and others added 22 commits April 29, 2023 17:01

add missing citations

d0b398c

update report rm plotly because of memory error

1798bcb

revert abundance and diversity without plotly

eecb3a4

do not ignore dowser errors

9e5ead6

parametrize find threshold

fd2d041

revert fixes for slurm size limit

e549b8a

fix find threshold report analysis

3900b52

revert parametrize findthreshold

de54d75

fix bug asString function call when no args

38da054

fix report reading tab

6245584

fix actions checkout

62f93a7

clean report comments

ac468d3

rm directcall igblast nasty workaround

3959525

Merge branch 'dev' into report-fix

aa6202b

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

1da9082

…-fix

Merge branch 'report-fix' of https://github.com/ggabernet/nf-core-air…

9cbd7d3

…rflow into report-fix

fix prettier

0deb76c

add check for whitespaces in columns

db1afb0

fix linting update changelog

7ee7461

rm to have igblast reassign the c_call

a1e4674

Merge pull request nf-core#258 from ggabernet/report-fix

b262243

Report fix and other bugfixes

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

b969a7a

ggabernet and others added 7 commits May 31, 2023 23:33

bump versions to 3.1.0

52d9983

Update changelog

2d1d5b6

Merge pull request nf-core#263 from ggabernet/dev

73112f9

bump versions to 3.1.0

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

25b3abe

Update conf/test_full.config

f648c0d

Co-authored-by: Maxime U Garcia <[email protected]>

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

ada49d0

clean up unnecessary quotes

0121f8e

ggabernet and others added 14 commits June 5, 2023 09:03

update to Enchantr 0.1.2

608e4e5

update nf-core modules

c0e430e

apply review comments

203f363

apply review comments

61e2954

update changelog

79dd465

[automated] Fix linting with Prettier

68ddf0a

Merge pull request nf-core#265 from ggabernet/enchantr-update

f235c82

Apply review corrections and tool version update

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

ggabernet marked this pull request as ready for review June 20, 2023 20:02

ggabernet commented Jun 20, 2023

View reviewed changes

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ggabernet and others added 5 commits June 20, 2023 16:07

Update assets/repertoire_comparison.Rmd

39f34a5

Update assets/repertoire_comparison.Rmd

9490ce0

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

ggabernet requested a review from ssnn-airr June 22, 2023 17:45

ggabernet changed the base branch from immcantation-devel to dev June 22, 2023 17:46

ggabernet changed the base branch from dev to immcantation-devel June 22, 2023 17:46

ssnn-airr reviewed Jun 22, 2023

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ssnn-airr reviewed Jun 22, 2023

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ssnn-airr reviewed Jun 22, 2023

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ssnn-airr approved these changes Jun 22, 2023

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ggabernet merged commit 7518036 into nf-core:immcantation-devel Jun 22, 2023

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Update immcantation-devel changes #260

Update immcantation-devel changes #260

ggabernet commented May 29, 2023

github-actions bot commented May 29, 2023 •

edited

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❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

ggabernet commented Jun 22, 2023

ssnn-airr Jun 22, 2023

ggabernet Jun 22, 2023

		@@ -22,7 +22,7 @@ process CHANGEO_PARSEDB_SELECT {
		def args2 = task.ext.args2 ?: ''
		if (meta.locus == 'IG'){

Update immcantation-devel changes #260

Update immcantation-devel changes #260

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ggabernet commented May 29, 2023

PR checklist

github-actions bot commented May 29, 2023 • edited Loading

nf-core lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

ggabernet commented Jun 22, 2023

ssnn-airr Jun 22, 2023

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ggabernet Jun 22, 2023

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github-actions bot commented May 29, 2023 •

edited

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