Template Update + cellranger functionality #315

mapo9 · 2024-03-23T10:11:12Z

This PR includes the ne template update.
It also introduces the possibility to analyse raw single cell data from 10xGenomics via the cellranger vdj tool

Remove FilterQuality silent fail

Fixes #292

…erge-template-updates

…_multiple_values clonal_threshold accepts multiple values in nextflow_schema.json

merge template updates

Fix sequence plot in airrflow report

Bump versions and update software versions

…erge-template-updates

Co-authored-by: Mark Polster <[email protected]>

…/nf-core-airrflow into merge-template-updates

updated nih url to add nlm

Template update nf-core tools 2.13.1

github-actions · 2024-03-23T10:12:57Z

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

Posted for pipeline commit df7ec7a

+| ✅ 204 tests passed       |+
#| ❔   7 tests were ignored |#
!| ❗   1 tests had warnings |!

❗ Test warnings:

nextflow_config - Config manifest.version should end in dev: 3.3.0

❔ 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.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 - .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: fix-linting.yml
actions_schema_validation - Workflow validation passed: linting_comment.yml
actions_schema_validation - Workflow validation passed: ci_immcantation.yml
actions_schema_validation - Workflow validation passed: clean-up.yml
actions_schema_validation - Workflow validation passed: branch.yml
actions_schema_validation - Workflow validation passed: ci.yml
actions_schema_validation - Workflow validation passed: release-announcements.yml
actions_schema_validation - Workflow validation passed: awsfulltest.yml
actions_schema_validation - Workflow validation passed: download_pipeline.yml
actions_schema_validation - Workflow validation passed: linting.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 2024-03-31 23:50:15

ggabernet

Looks good to me, I'll fix the download problem in the next release as this will take some time to solve and it would be good to release the current bugfixes and features!

CHANGELOG.md

ggabernet and others added 30 commits November 21, 2023 09:25

rm optional true from filterquality

efd6bca

bump versions 3.2.1dev

500a21e

Merge pull request #287 from ggabernet/dev

51b7506

Remove FilterQuality silent fail

fixed comment

f8f958c

split bulk/sc raw

385364c

added cellranger reference, cellranger vdj

5c3f677

added cellranger vdj

e53237d

added cellranger vdj

f35e3d7

set detect contamination false

bda513b

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

f72a66b

rm unnecessary ifEmpty

671738e

Template update for nf-core/tools version 2.11

5edf4d0

Template update for nf-core/tools version 2.11.1

f7b2273

clonal_threshold validation uses JSON schema format

65a1e89

Fixes #292

cheat linter with extra 'type' entry

2915e70

merge upstream dev

820e38e

fix docker emulation

17470ca

fix schema linting

adbdd1a

making @maxulysse happy

35463cb

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

428151f

…erge-template-updates

rm unused genome param

58f09e6

Merge pull request #293 from adamrtalbot/292_clonal_threshold_accepts…

4222d35

…_multiple_values clonal_threshold accepts multiple values in nextflow_schema.json

Merge branch 'dev' into merge-template-updates

8b1ebdb

Merge pull request #294 from ggabernet/merge-template-updates

47e2483

merge template updates

add nebnext profile

a78999b

add clontech umi protocol

507a3d3

add nebnext and clontech protocols

e4d1f5d

improve report

5479451

update changelog

3112077

Merge pull request #295 from ggabernet/dev

987fc69

Fix sequence plot in airrflow report

ggabernet and others added 22 commits March 11, 2024 15:38

update nf-core modules versions

6bbc21d

update airrflow images

2a55194

Merge branch 'dev' into dev

afb1b48

update changelog

710d590

update igblast mulled containers

f8e4c6b

specify isotype column

1eec97e

fix isotype column

b6f0bec

add default isotype column

a8944b5

Merge pull request #310 from ggabernet/dev

699948a

Bump versions and update software versions

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

c09ec38

…erge-template-updates

updated nih url to add nlm

33f8a45

add citation

70802ce

fix samplesheet template update

ca57b90

add missing versions fix linting

7df46af

Update main.nf

7f2f56c

Co-authored-by: Mark Polster <[email protected]>

apply harshil-alignmentTM

1366083

add and clean citations

a37b117

Merge branch 'merge-template-updates' of https://github.com/ggabernet…

56db166

…/nf-core-airrflow into merge-template-updates

rm quotes references

3b13f7b

Merge pull request #313 from immcantation/dev

4caa8da

updated nih url to add nlm

fix reference list

cb7113d

Merge pull request #314 from ggabernet/merge-template-updates

9d1d580

Template update nf-core tools 2.13.1

ggabernet approved these changes Mar 28, 2024

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ggabernet requested a review from ssnn-airr March 29, 2024 01:35

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ssnn-airr approved these changes Mar 29, 2024

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ggabernet reviewed Mar 31, 2024

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ggabernet merged commit 3750647 into master Mar 31, 2024
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Template Update + cellranger functionality #315

Template Update + cellranger functionality #315

mapo9 commented Mar 23, 2024

github-actions bot commented Mar 23, 2024 •

edited

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❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

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ggabernet left a comment

Template Update + cellranger functionality #315

Template Update + cellranger functionality #315

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mapo9 commented Mar 23, 2024

github-actions bot commented Mar 23, 2024 • edited Loading

nf-core lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

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github-actions bot commented Mar 23, 2024 •

edited

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