Release 4.1 #337

ggabernet · 2024-05-30T21:06:42Z

PR checklist

…erge-template-updates

Fix report plots

Immcantation version bump

github-actions · 2024-05-30T21:08:32Z

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

Posted for pipeline commit df9ca20

+| ✅ 270 tests passed       |+
#| ❔   7 tests were ignored |#
!| ❗   1 tests had warnings |!

❗ Test warnings:

nextflow_config - Config manifest.version should end in dev: 4.1.0

❔ 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 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: .github/workflows/push_dockerhub.yml
files_exist - File not found check: .markdownlint.yml
files_exist - File not found check: .nf-core.yaml
files_exist - File not found check: .yamllint.yml
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: docs/images/nf-core-airrflow_logo.png
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/NfcoreTemplate.groovy
files_exist - File not found check: lib/Utils.groovy
files_exist - File not found check: lib/Workflow.groovy
files_exist - File not found check: lib/WorkflowMain.groovy
files_exist - File not found check: lib/WorkflowAirrflow.groovy
files_exist - File not found check: parameters.settings.json
files_exist - File not found check: pipeline_template.yml
files_exist - File not found check: Singularity
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
nextflow_config - Config default value correct: params.pipelines_testdata_base_path= https://raw.githubusercontent.com/nf-core/test-datasets/airrflow/
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
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 (216 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: branch.yml
actions_schema_validation - Workflow validation passed: ci.yml
actions_schema_validation - Workflow validation passed: awsfulltest.yml
actions_schema_validation - Workflow validation passed: fix-linting.yml
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: download_pipeline.yml
actions_schema_validation - Workflow validation passed: release-announcements.yml
actions_schema_validation - Workflow validation passed: clean-up.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_immcantation.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 found and not ignored.
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'
base_config - conf/base.config found and not ignored.
modules_config - conf/modules.config found and not ignored.
modules_config - SAMPLESHEET_CHECK found in conf/modules.config and Nextflow scripts.
modules_config - SAMPLESHEET_CHECK_ASSEMBLED found in conf/modules.config and Nextflow scripts.
modules_config - FASTP found in conf/modules.config and Nextflow scripts.
modules_config - GUNZIP_ found in conf/modules.config and Nextflow scripts.
modules_config - VALIDATE_INPUT found in conf/modules.config and Nextflow scripts.
modules_config - FASTQC found in conf/modules.config and Nextflow scripts.
modules_config - FASTQC_POSTASSEMBLY found in conf/modules.config and Nextflow scripts.
modules_config - RENAME_FASTQ found in conf/modules.config and Nextflow scripts.
modules_config - RENAME_FILE_ found in conf/modules.config and Nextflow scripts.
modules_config - MERGE_UMI found in conf/modules.config and Nextflow scripts.
modules_config - PRESTO_FILTERSEQ found in conf/modules.config and Nextflow scripts.
modules_config - PRESTO_FILTERSEQ_POSTASSEMBLY_SANS_UMI found in conf/modules.config and Nextflow scripts.
modules_config - PRESTO_MASKPRIMERS_UMI found in conf/modules.config and Nextflow scripts.
modules_config - PRESTO_MASKPRIMERS_ALIGN found in conf/modules.config and Nextflow scripts.
modules_config - PRESTO_ALIGN_CREGION found in conf/modules.config and Nextflow scripts.
modules_config - PRESTO_MASKPRIMERS_EXTRACT found in conf/modules.config and Nextflow scripts.
modules_config - PRESTO_MASKPRIMERS_POSTASSEMBLY_SANS_UMI found in conf/modules.config and Nextflow scripts.
modules_config - PRESTO_PAIRSEQ found in conf/modules.config and Nextflow scripts.
modules_config - PRESTO_PAIRSEQ_ALIGN found in conf/modules.config and Nextflow scripts.
modules_config - PRESTO_CLUSTERSETS found in conf/modules.config and Nextflow scripts.
modules_config - PRESTO_PARSE_CLUSTER found in conf/modules.config and Nextflow scripts.
modules_config - PRESTO_BUILDCONSENSUS_UMI found in conf/modules.config and Nextflow scripts.
modules_config - PRESTO_BUILDCONSENSUS_ALIGN found in conf/modules.config and Nextflow scripts.
modules_config - PRESTO_POSTCONSENSUS_PAIRSEQ found in conf/modules.config and Nextflow scripts.
modules_config - PRESTO_ASSEMBLEPAIRS_UMI found in conf/modules.config and Nextflow scripts.
modules_config - PRESTO_ASSEMBLEPAIRS_SEQUENTIAL found in conf/modules.config and Nextflow scripts.
modules_config - PRESTO_ASSEMBLEPAIRS_SANS_UMI found in conf/modules.config and Nextflow scripts.
modules_config - PRESTO_PARSEHEADERS_COLLAPSE_UMI found in conf/modules.config and Nextflow scripts.
modules_config - PRESTO_PARSEHEADERS_PRIMERS_UMI found in conf/modules.config and Nextflow scripts.
modules_config - PRESTO_PARSEHEADERS_CREGION found in conf/modules.config and Nextflow scripts.
modules_config - PRESTO_PARSEHEADERS_PRIMERS_SANS_UMI found in conf/modules.config and Nextflow scripts.
modules_config - PRESTO_PARSEHEADERS_METADATA found in conf/modules.config and Nextflow scripts.
modules_config - PRESTO_COLLAPSESEQ_UMI found in conf/modules.config and Nextflow scripts.
modules_config - PRESTO_COLLAPSESEQ_ALIGN found in conf/modules.config and Nextflow scripts.
modules_config - PRESTO_COLLAPSESEQ_CREGION found in conf/modules.config and Nextflow scripts.
modules_config - PRESTO_COLLAPSESEQ_SANS_UMI found in conf/modules.config and Nextflow scripts.
modules_config - PRESTO_SPLITSEQ_UMI found in conf/modules.config and Nextflow scripts.
modules_config - PRESTO_SPLITSEQ_SANS_UMI found in conf/modules.config and Nextflow scripts.
modules_config - FETCH_DATABASES found in conf/modules.config and Nextflow scripts.
modules_config - UNZIP_DB found in conf/modules.config and Nextflow scripts.
modules_config - CHANGEO_CONVERTDB_FASTA_FROM_AIRR found in conf/modules.config and Nextflow scripts.
modules_config - CHANGEO_ASSIGNGENES found in conf/modules.config and Nextflow scripts.
modules_config - CHANGEO_MAKEDB found in conf/modules.config and Nextflow scripts.
modules_config - FILTER_QUALITY found in conf/modules.config and Nextflow scripts.
modules_config - CHANGEO_PARSEDB_SPLIT found in conf/modules.config and Nextflow scripts.
modules_config - FILTER_JUNCTION_MOD3 found in conf/modules.config and Nextflow scripts.
modules_config - ADD_META_TO_TAB found in conf/modules.config and Nextflow scripts.
modules_config - CHANGEO_CREATEGERMLINES found in conf/modules.config and Nextflow scripts.
modules_config - REMOVE_CHIMERIC found in conf/modules.config and Nextflow scripts.
modules_config - DETECT_CONTAMINATION found in conf/modules.config and Nextflow scripts.
modules_config - COLLAPSE_DUPLICATES found in conf/modules.config and Nextflow scripts.
modules_config - SINGLE_CELL_QC found in conf/modules.config and Nextflow scripts.
modules_config - FIND_CLONAL_THRESHOLD found in conf/modules.config and Nextflow scripts.
modules_config - REPORT_THRESHOLD found in conf/modules.config and Nextflow scripts.
modules_config - DEFINE_CLONES_COMPUTE found in conf/modules.config and Nextflow scripts.
modules_config - DEFINE_CLONES_REPORT found in conf/modules.config and Nextflow scripts.
modules_config - DOWSER_LINEAGES found in conf/modules.config and Nextflow scripts.
modules_config - AIRRFLOW_REPORT found in conf/modules.config and Nextflow scripts.
modules_config - PARSE_LOGS found in conf/modules.config and Nextflow scripts.
modules_config - REPORT_FILE_SIZE found in conf/modules.config and Nextflow scripts.
modules_config - MULTIQC found in conf/modules.config and Nextflow scripts.
nfcore_yml - Repository type in .nf-core.yml is valid: pipeline
nfcore_yml - nf-core version in .nf-core.yml is set to the latest version: 2.14.1

Run details

nf-core/tools version 2.14.1
Run at 2024-06-01 00:20:45

nextflow_schema.json

nextflow.config

maxulysse

Minor suggestions about what I think should be the proper usage for this params

JoseEspinosa

Awesome! 👍
Only minor comments and it seems that one test is failing, feel free to merge after addressing them 🚀

nextflow.config

docs/usage.md

modules/local/airrflow_report/airrflow_report.nf

Co-authored-by: Jose Espinosa-Carrasco <[email protected]>

Apply PR review comments

Co-authored-by: Jose Espinosa-Carrasco <[email protected]>

ggabernet · 2024-05-31T20:04:35Z

Awesome! 👍 Only minor comments and it seems that one test is failing, feel free to merge after addressing them 🚀

Not sure why the download workflow pull_request_target is failing, but the pull_request one is passing! So I think we're good to go

nf-core-bot and others added 23 commits May 8, 2024 13:58

Template update for nf-core/tools version 2.14.0

63cb94d

Template update for nf-core/tools version 2.14.1

0788d44

try fix report file size

46f8eb6

fix sequence number plot

4401e8c

update changelog

bdaf234

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

f2c1a4a

…erge-template-updates

update testdata base path

50df308

rm custom software versions

22f410d

solve warning

ee7c264

fix testdata path param

140cc54

rm monochromelog warning

69c626f

update old container biopython

967b3b7

revert monochrome logs as nf-core lint fails

094f254

Merge pull request #335 from ggabernet/dev

7b0cdc3

Fix report plots

update container airrflow 4.1.0

236e0f9

test the dev container

0c72700

update container

7101a6d

update changelog

7304208

improve protocol logs

d933c48

presto wasnt updated

cf55590

fix linting

fa5664e

rm irrelevant param

032a56d

Merge pull request #336 from ggabernet/dev

61cdcd8

Immcantation version bump

maxulysse reviewed May 31, 2024

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maxulysse reviewed May 31, 2024

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nextflow.config Outdated Show resolved Hide resolved

maxulysse reviewed May 31, 2024

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maxulysse approved these changes May 31, 2024

View reviewed changes

JoseEspinosa approved these changes May 31, 2024

View reviewed changes

Update docs/usage.md

dec79a9

Co-authored-by: Jose Espinosa-Carrasco <[email protected]>

ggabernet and others added 11 commits May 31, 2024 15:30

add tutorial

39d5270

simplify container

efda2c4

update test data param

0d30d4c

Merge pull request #338 from ggabernet/dev

b14fe8c

Apply PR review comments

update reference defaluts

3c20ec3

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

6f89abf

merge upstream

6da9c38

Update docs/usage.md

acbdfc9

Co-authored-by: Jose Espinosa-Carrasco <[email protected]>

update default in schema

0cd3f18

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

b7bceb7

merge upstream

4e1c52b

ggabernet added 2 commits May 31, 2024 20:15

allow skip multiqc

affd98d

update tutorial script

df9ca20

ggabernet merged commit 0c0bcde into master Jun 1, 2024
46 of 47 checks passed

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Release 4.1 #337

Release 4.1 #337

ggabernet commented May 30, 2024

github-actions bot commented May 30, 2024 •

edited

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❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

maxulysse left a comment

JoseEspinosa left a comment

ggabernet commented May 31, 2024

Release 4.1 #337

Release 4.1 #337

Conversation

ggabernet commented May 30, 2024

PR checklist

github-actions bot commented May 30, 2024 • edited Loading

nf-core lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

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ggabernet commented May 31, 2024

github-actions bot commented May 30, 2024 •

edited

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