Release 4.0.0 #325

mapo9 · 2024-04-22T14:17:50Z

PR checklist

Fix badges in master

Minor bug fixes

Dowser tips by isotype

github-actions · 2024-04-22T14:19:37Z

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

Posted for pipeline commit 8e90b1f

+| ✅ 205 tests passed       |+
#| ❔   7 tests were ignored |#
!| ❗   1 tests had warnings |!

❗ Test warnings:

nextflow_config - Config manifest.version should end in dev: 4.0

❔ Tests ignored:

files_exist - File is ignored: conf/igenomes.config
nextflow_config - Config default ignored: params.miairr
nextflow_config - Config default ignored: params.report_rmd
nextflow_config - Config default ignored: params.report_css
nextflow_config - Config default ignored: params.report_logo
nextflow_config - Config default ignored: params.report_logo_img
nextflow_config - Config default ignored: params.config_profile_url

✅ 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: 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: 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: 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: 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/WorkflowAirrflow.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.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/
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.mode= fastq
nextflow_config - Config default value correct: params.vprimer_start= 0
nextflow_config - Config default value correct: params.cprimer_start= 0
nextflow_config - Config default value correct: params.cprimer_position= R1
nextflow_config - Config default value correct: params.umi_position= R1
nextflow_config - Config default value correct: params.umi_length= -1
nextflow_config - Config default value correct: params.umi_start= 0
nextflow_config - Config default value correct: params.trim_fastq= true
nextflow_config - Config default value correct: params.clip_r1= 0
nextflow_config - Config default value correct: params.clip_r2= 0
nextflow_config - Config default value correct: params.three_prime_clip_r1= 0
nextflow_config - Config default value correct: params.three_prime_clip_r2= 0
nextflow_config - Config default value correct: params.filterseq_q= 20
nextflow_config - Config default value correct: params.primer_consensus= 0.6
nextflow_config - Config default value correct: params.primer_mask_mode= cut
nextflow_config - Config default value correct: params.buildconsensus_maxerror= 0.1
nextflow_config - Config default value correct: params.buildconsensus_maxgap= 0.5
nextflow_config - Config default value correct: params.cluster_sets= true
nextflow_config - Config default value correct: params.primer_r1_maxerror= 0.2
nextflow_config - Config default value correct: params.primer_r2_maxerror= 0.2
nextflow_config - Config default value correct: params.primer_extract_len= 0
nextflow_config - Config default value correct: params.primer_maxlen= 50
nextflow_config - Config default value correct: params.cregion_maxlen= 100
nextflow_config - Config default value correct: params.cregion_maxerror= 0.3
nextflow_config - Config default value correct: params.cregion_mask_mode= tag
nextflow_config - Config default value correct: params.reassign= true
nextflow_config - Config default value correct: params.productive_only= true
nextflow_config - Config default value correct: params.isotype_column= c_call
nextflow_config - Config default value correct: params.collapseby= sample_id
nextflow_config - Config default value correct: params.clonal_threshold= auto
nextflow_config - Config default value correct: params.cloneby= subject_id
nextflow_config - Config default value correct: params.crossby= subject_id
nextflow_config - Config default value correct: params.lineage_tree_builder= raxml
nextflow_config - Config default value correct: params.lineage_tree_exec= /usr/local/bin/raxml-ng
nextflow_config - Config default value correct: params.singlecell= single_cell
nextflow_config - Config default value correct: params.igenomes_base= s3://ngi-igenomes/igenomes
nextflow_config - Config default value correct: params.igenomes_ignore= true
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 - 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 - .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_todos - No TODO strings found
pipeline_name_conventions - Name adheres to nf-core convention
template_strings - Did not find any Jinja template strings (215 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: awstest.yml
actions_schema_validation - Workflow validation passed: branch.yml
actions_schema_validation - Workflow validation passed: ci.yml
actions_schema_validation - Workflow validation passed: clean-up.yml
actions_schema_validation - Workflow validation passed: fix-linting.yml
actions_schema_validation - Workflow validation passed: ci_immcantation.yml
actions_schema_validation - Workflow validation passed: release-announcements.yml
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: awsfulltest.yml
actions_schema_validation - Workflow validation passed: linting_comment.yml
actions_schema_validation - Workflow validation passed: download_pipeline.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 2024-04-23 13:09:28

Make RAxML default, use profile for full size test

Revert changes test_full

Fix test full profile

Update germline reference parameters

ggabernet

Looks good to me

ssnn-airr

LGTM

ggabernet added 23 commits March 31, 2024 17:58

Merge pull request #317 from nf-core/master

16a4c0e

Fix badges in master

fix test full run

271b4bd

fix nebnext_umi_tcr profile

6205b75

update changelog

e29cfda

fix execute parse logs

6554b2e

add airr compliance badge

87845c0

Add description AIRR compliant

8d50033

Merge pull request #319 from ggabernet/dev

e19ba5e

Minor bug fixes

Dowser tips by isotype

4434024

update changelog

6947cf6

isotype also for full test

1bdaf4c

Merge pull request #321 from ggabernet/dev

e6eacdd

Dowser tips by isotype

use raxml by default

96a0338

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

0df52e4

fix test full config

3ee7e7c

update enchantr version

5a8432b

fix prettier

fe3eb08

more raxml changes

b56d929

add profile info to readme

22a21d9

fix comma

fb72bff

skip lineage trees by default

9739fcd

change version to 4.0.0

ffb761a

oops fix container tag

43cf4d5

Merge pull request #324 from ggabernet/dev

1402385

Make RAxML default, use profile for full size test

ggabernet changed the title ~~Dev~~ Release 4.0.0 Apr 22, 2024

ggabernet added 4 commits April 22, 2024 18:32

revert changes test full

4003891

Merge pull request #327 from ggabernet/dev

ee4391c

Revert changes test_full

Deprecate igblast_base and imgtdb_base params

a376dc2

fix full size test

e598df3

ggabernet added 5 commits April 22, 2024 20:59

fix test full

55c0157

Merge pull request #329 from ggabernet/fix-profile

2345dda

Fix test full profile

Merge upstream dev

b65e2eb

update unzip fasta name

553f317

Merge pull request #328 from ggabernet/dev

8e90b1f

Update germline reference parameters

ggabernet requested a review from ssnn-airr April 23, 2024 13:08

ggabernet approved these changes Apr 23, 2024

View reviewed changes

ssnn-airr approved these changes Apr 23, 2024

View reviewed changes

ggabernet merged commit 2f492b0 into master Apr 23, 2024
42 of 46 checks passed

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Release 4.0.0 #325

Release 4.0.0 #325

mapo9 commented Apr 22, 2024

github-actions bot commented Apr 22, 2024 •

edited

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❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

ggabernet left a comment

ssnn-airr left a comment

Release 4.0.0 #325

Release 4.0.0 #325

Conversation

mapo9 commented Apr 22, 2024

PR checklist

github-actions bot commented Apr 22, 2024 • edited Loading

nf-core lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

ggabernet left a comment

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github-actions bot commented Apr 22, 2024 •

edited

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