Provide profile for NEB and TAKARA protocols #299

ggabernet · 2024-01-19T23:05:49Z

PR checklist

github-actions · 2024-01-19T23:07:29Z

`nf-core lint` overall result: Passed ✅

Posted for pipeline commit affe6b6

+| ✅ 205 tests passed       |+
#| ❔   7 tests were ignored |#

❔ 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: 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: 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/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 manifest.version ends in dev: 3.2.1dev
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.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.igphyml= /usr/local/share/igphyml/src/igphyml
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 - 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_todos - No TODO strings found
pipeline_name_conventions - Name adheres to nf-core convention
template_strings - Did not find any Jinja template strings (185 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: awstest.yml
actions_schema_validation - Workflow validation passed: linting.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: awsfulltest.yml
actions_schema_validation - Workflow validation passed: linting_comment.yml
actions_schema_validation - Workflow validation passed: download_pipeline.yml
actions_schema_validation - Workflow validation passed: ci_immcantation.yml
actions_schema_validation - Workflow validation passed: release-announcements.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 2.12.1
Run at 2024-02-16 14:59:17

ggabernet · 2024-02-14T23:01:00Z

All the tests are passing except the ones using the Immcantation container 👍

typo

ggabernet added 7 commits January 8, 2024 13:41

add nebnext profile

a78999b

add clontech umi protocol

507a3d3

add nebnext and clontech protocols

e4d1f5d

update assemblepairs sequential container

9e3a7ea

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

13ac285

work on protocols

043dcb0

maskprimers separate R1 and R2

b113679

ggabernet added 5 commits January 19, 2024 18:08

fix black formating

5b6e02f

add cregion alignment

6d96816

work on clontech umi profile

b766ac5

add param schema

9bd4633

add protocols documentation

4ae4b1b

ggabernet marked this pull request as ready for review February 5, 2024 18:19

ggabernet changed the base branch from dev to master February 5, 2024 18:20

ggabernet changed the base branch from master to dev February 5, 2024 18:21

ggabernet added 8 commits February 13, 2024 21:14

add test profiles

7691cf9

add tests to ci

306024b

add test to ci workflow

c1334bc

fix test configs

8cbae05

fix prettier

2376f16

update test config

62554ca

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

9832970

fix precommit

3af5e59

ggabernet requested a review from ssnn-airr February 14, 2024 23:00

Update usage.md

affe6b6

typo

ssnn-airr approved these changes Feb 16, 2024

View reviewed changes

ggabernet merged commit 06bbaad into nf-core:dev Feb 16, 2024
20 of 26 checks passed

ggabernet deleted the protocols branch November 27, 2024 01:11

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Provide profile for NEB and TAKARA protocols #299

Provide profile for NEB and TAKARA protocols #299

ggabernet commented Jan 19, 2024

github-actions bot commented Jan 19, 2024 •

edited

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❔ Tests ignored:

✅ Tests passed:

Run details

ggabernet commented Feb 14, 2024

Provide profile for NEB and TAKARA protocols #299

Provide profile for NEB and TAKARA protocols #299

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ggabernet commented Jan 19, 2024

PR checklist

github-actions bot commented Jan 19, 2024 • edited Loading

nf-core lint overall result: Passed ✅

❔ Tests ignored:

✅ Tests passed:

Run details

ggabernet commented Feb 14, 2024

github-actions bot commented Jan 19, 2024 •

edited

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`nf-core lint` overall result: Passed ✅