Release 4.2.0 #358

ggabernet · 2024-11-26T14:58:59Z

Adds TRUST4 support
Adds options to remove V and C primer region by length when primer sequences are unknown.
Adds option to save non-productive sequences after IgBlast alignment.
Updated nf-core template to v3.0.2
Deprecated isotype_column param in favor of annotating C region or C primer information in the c_call column when c_call is NA.
Avoids saving pRESTO intermediate files in results directory to save space.
Simplified pRESTO Maskprimers score and Maskprimers extract processes.
Fix clustersets approach, consider both reads clusters annotation.
Allow for partial alignments in MakeDB for mouse TCR data, to bypass junction check for TRAV germlines with additional positions (e.g. 84A).
Fix parse logs merging dataframes using pandas join to produce logs even when there are failing samples.
Use pRESTO Collapseseq with n=0 by default to improve runtime.

…nto trust4

Prepare release 4.2.0

github-actions · 2024-11-26T15:01:03Z

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

Posted for pipeline commit 91449a8

+| ✅ 300 tests passed       |+
#| ❔   8 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
included_configs - included_configs

✅ 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: conf/igenomes_ignored.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 - Found nf-schema plugin
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: validation.help.enabled
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 found: validation.help.beforeText
nextflow_config - Config variable found: validation.help.afterText
nextflow_config - Config variable found: validation.help.command
nextflow_config - Config variable found: validation.summary.beforeText
nextflow_config - Config variable found: validation.summary.afterText
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 variable (correctly) not found: params.max_cpus
nextflow_config - Config variable (correctly) not found: params.max_memory
nextflow_config - Config variable (correctly) not found: params.max_time
nextflow_config - Config variable (correctly) not found: params.validationFailUnrecognisedParams
nextflow_config - Config variable (correctly) not found: params.validationLenientMode
nextflow_config - Config variable (correctly) not found: params.validationSchemaIgnoreParams
nextflow_config - Config variable (correctly) not found: params.validationShowHiddenParams
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 does not contain dev for release: 4.2.0
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.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_maxlen= 50
nextflow_config - Config default value correct: params.primer_r1_mask_mode= cut
nextflow_config - Config default value correct: params.primer_r2_mask_mode= cut
nextflow_config - Config default value correct: params.primer_r1_extract_len= 0
nextflow_config - Config default value correct: params.primer_r2_extract_len= 0
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.save_databases= true
nextflow_config - Config default value correct: params.reference_fasta= https://raw.githubusercontent.com/nf-core/test-datasets/airrflow/database-cache/imgtdb_base.zip
nextflow_config - Config default value correct: params.reference_igblast= https://raw.githubusercontent.com/nf-core/test-datasets/airrflow/database-cache/igblast_base.zip
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_ignore= true
nextflow_config - Config default value correct: params.igenomes_base= s3://ngi-igenomes/igenomes/
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.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: 24.04.2, Config: 24.04.2
readme - README Zenodo placeholder was replaced with DOI.
pipeline_todos - No TODO strings found
plugin_includes - No wrong validation plugin imports have been found
pipeline_name_conventions - Name adheres to nf-core convention
template_strings - Did not find any Jinja template strings (0 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: linting.yml
actions_schema_validation - Workflow validation passed: branch.yml
actions_schema_validation - Workflow validation passed: fix-linting.yml
actions_schema_validation - Workflow validation passed: release-announcements.yml
actions_schema_validation - Workflow validation passed: awsfulltest.yml
actions_schema_validation - Workflow validation passed: template_version_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: ci.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
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_SCORE_UMI_R1 found in conf/modules.config and Nextflow scripts.
modules_config - PRESTO_MASKPRIMERS_SCORE_UMI_R2 found in conf/modules.config and Nextflow scripts.
modules_config - PRESTO_ALIGN_PRIMERS 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_ALIGN_UMI_R1 found in conf/modules.config and Nextflow scripts.
modules_config - PRESTO_MASKPRIMERS_ALIGN_UMI_R2 found in conf/modules.config and Nextflow scripts.
modules_config - PRESTO_MASKPRIMERS_EXTRACT_R1 found in conf/modules.config and Nextflow scripts.
modules_config - PRESTO_MASKPRIMERS_EXTRACT_R2 found in conf/modules.config and Nextflow scripts.
modules_config - PRESTO_MASKPRIMERS_SCORE_SANSUMI_FWD found in conf/modules.config and Nextflow scripts.
modules_config - PRESTO_MASKPRIMERS_SCORE_SANSUMI_REV found in conf/modules.config and Nextflow scripts.
modules_config - PRESTO_MASKPRIMERS_ALIGN_SANSUMI_FWD found in conf/modules.config and Nextflow scripts.
modules_config - PRESTO_MASKPRIMERS_ALIGN_SANSUMI_REV 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_PAIRSEQ_EXTRACT found in conf/modules.config and Nextflow scripts.
modules_config - PRESTO_CLUSTERSETS_UMI found in conf/modules.config and Nextflow scripts.
modules_config - PRESTO_PARSE_CLUSTER found in conf/modules.config and Nextflow scripts.
modules_config - PRESTO_PAIRSEQ_CLUSTERSETS 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_RACE found in conf/modules.config and Nextflow scripts.
modules_config - PRESTO_BUILDCONSENSUS_EXTRACT 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_ 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_SELECT_LOCUS 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: 3.0.2
version_consistency - Version tags are numeric and consistent between container, release tag and config.

Run details

nf-core/tools version 3.0.2
Run at 2024-12-10 21:00:41

assets/multiqc_config.yml

conf/test_maskprimers_align.config

mapo9

lgtm! 🚀

mapo9 · 2024-11-27T07:55:14Z

README.md

- [Friederike Hanssen](https://github.com/ggabernet/friederikehanssen)
+- [Friederike Hanssen](https://github.com/friederikehanssen)
+- [Simon Heumos](https://github.com/subwaystation)
+- [Mark Polster](https://github.com/mapo9)


thanks for that :D

of course, I thought you were already there

Remove conda CI tests

ggabernet · 2024-11-27T17:36:45Z

Do not merge yet, as TRUST4 should be added to the pipeline diagram!

.nf-core.yml

ssnn-airr

LGTM

mapo9 · 2024-11-28T06:52:18Z

Do not merge yet, as TRUST4 should be added to the pipeline diagram!

I can make a metromap where I remove MiXCR and have only TRUST4 later today

mapo9 · 2024-11-28T08:26:11Z

@ggabernet I added the metromap directly to this pr. Please check it out

Update pipeline diagrams

mapo9 and others added 30 commits March 21, 2024 13:15

first steps & sc run

11c4195

input change

6639f0f

stage before pull

2a42c32

Merge remote-tracking branch 'origin/master' into dev

9d2c18a

merged most recent airrflow version

47a7642

barcode airr test

a5af202

dev update

48e1b68

Merge branch 'master' of https://github.com/mapo9/airrflow into trust4

e434be7

skip presto reporting which doesnt happen when trust4 is used

6242a6f

linting

761eccc

fastp before trust4

2da37e2

fastp before trust4

d262a38

bulk and sc rnaseq input

50418e1

bulk rnaseq test workflow

c6f95bf

sc rnaseq tests

c72146c

docs

7746378

linting & prettier

5ef2f60

trailing whitespace

0bc5c19

trailing whitespace

82c0688

bugfix

1a3a629

trailing whitespace

d822084

view statement removed

90cada8

incorporating review comments

35cf7f4

fix test

cbdc415

removed view statement

948bb53

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

f13eeab

…nto trust4

generate reference fasta

616349f

channel in wrong subworkflow

9443bc8

generate trust4 reference

310e302

Merge branch 'dev' of https://github.com/nf-core/airrflow into trust4

b9e977f

ggabernet added 3 commits November 25, 2024 21:23

update changelog

9c0e84b

bump enchantr version

4dbb78a

Merge pull request #357 from ggabernet/dev

4b9d1db

Prepare release 4.2.0

ggabernet requested review from mapo9 and ssnn-airr November 26, 2024 14:59

ssnn-airr reviewed Nov 26, 2024

View reviewed changes

assets/multiqc_config.yml Outdated Show resolved Hide resolved

ssnn-airr reviewed Nov 26, 2024

View reviewed changes

conf/test_maskprimers_align.config Outdated Show resolved Hide resolved

ggabernet added 2 commits November 26, 2024 15:14

rm conda from ci tests

b7c2159

apply reviewer suggestions

106fc44

mapo9 approved these changes Nov 27, 2024

View reviewed changes

Merge pull request #359 from ggabernet/dev

f47c846

Remove conda CI tests

ggabernet requested a review from ssnn-airr November 27, 2024 17:35

ggabernet added the do not merge label Nov 27, 2024

ggabernet commented Nov 27, 2024

View reviewed changes

.nf-core.yml Show resolved Hide resolved

Update .nf-core.yml

3b5ef6f

ssnn-airr approved these changes Nov 27, 2024

View reviewed changes

mapo9 closed this Nov 28, 2024

mapo9 reopened this Nov 28, 2024

metro map including trust4

548709c

ggabernet added 6 commits December 8, 2024 21:08

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

bb59c7a

update metro map

2ad7bea

update workflow overview

362b558

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

4fcc4af

Merge pull request #360 from ggabernet/dev

6637452

Update pipeline diagrams

fix ci setup nextfow

91449a8

ggabernet merged commit d91dd84 into master Dec 11, 2024
66 of 67 checks passed

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

Release 4.2.0 #358

Release 4.2.0 #358

ggabernet commented Nov 26, 2024

github-actions bot commented Nov 26, 2024 •

edited

Loading

❔ Tests ignored:

✅ Tests passed:

Run details

mapo9 left a comment

mapo9 Nov 27, 2024

ggabernet Nov 27, 2024

ggabernet commented Nov 27, 2024

ssnn-airr left a comment

mapo9 commented Nov 28, 2024

mapo9 commented Nov 28, 2024

Release 4.2.0 #358

Release 4.2.0 #358

Conversation

ggabernet commented Nov 26, 2024

github-actions bot commented Nov 26, 2024 • edited Loading

nf-core pipelines lint overall result: Passed ✅

❔ Tests ignored:

✅ Tests passed:

Run details

mapo9 left a comment

Choose a reason for hiding this comment

mapo9 Nov 27, 2024

Choose a reason for hiding this comment

ggabernet Nov 27, 2024

Choose a reason for hiding this comment

ggabernet commented Nov 27, 2024

ssnn-airr left a comment

Choose a reason for hiding this comment

mapo9 commented Nov 28, 2024

mapo9 commented Nov 28, 2024

github-actions bot commented Nov 26, 2024 •

edited

Loading

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