Refactor references #505

rannick · 2024-10-16T07:28:47Z

PR checklist

This comment contains a description of changes (with reason).
If you've fixed a bug or added code that should be tested, add tests!
If you've added a new tool - have you followed the pipeline conventions in the contribution docs
If necessary, also make a PR on the nf-core/rnafusion branch on the nf-core/test-datasets repository.
Make sure your code lints (nf-core lint).

Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <OUTDIR>).
Usage Documentation in docs/usage.md is updated.
Output Documentation in docs/output.md is updated.
CHANGELOG.md is updated.
README.md is updated (including new tool citations and authors/contributors).

…tor-references

github-actions · 2024-10-16T07:28:59Z

Warning

Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 3.0.2.
Please update your pipeline to the latest version.

For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation.

apeltzer · 2024-11-07T12:46:11Z

Anything we can help here @rannick ?

github-actions · 2024-11-13T13:22:00Z

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

Posted for pipeline commit 31b400a

+| ✅ 221 tests passed       |+
#| ❔   2 tests were ignored |#

❔ Tests ignored:

files_unchanged - File ignored due to lint config: .github/CONTRIBUTING.md
files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md

✅ 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-rnafusion_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-rnafusion_logo_light.png
files_exist - File found: docs/images/nf-core-rnafusion_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.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-rnafusion_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/WorkflowRnafusion.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 ends in dev: 4.0.0dev
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.read_length= 100
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/
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/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/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-rnafusion_logo_light.png matches the template
files_unchanged - docs/images/nf-core-rnafusion_logo_light.png matches the template
files_unchanged - docs/images/nf-core-rnafusion_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.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 a matching 'report_comment'.
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 - ARRIBA_ARRIBA found in conf/modules.config and Nextflow scripts.
modules_config - ARRIBA_DOWNLOAD found in conf/modules.config and Nextflow scripts.
modules_config - ARRIBA_VISUALISATION found in conf/modules.config and Nextflow scripts.
modules_config - GENCODE_DOWNLOAD found in conf/modules.config and Nextflow scripts.
modules_config - FASTP found in conf/modules.config and Nextflow scripts.
modules_config - FASTQC found in conf/modules.config and Nextflow scripts.
modules_config - FASTQC_FOR_FASTP found in conf/modules.config and Nextflow scripts.
modules_config - FUSIONCATCHER found in conf/modules.config and Nextflow scripts.
modules_config - FUSIONCATCHER_DOWNLOAD found in conf/modules.config and Nextflow scripts.
modules_config - FUSIONINSPECTOR found in conf/modules.config and Nextflow scripts.
modules_config - FUSIONREPORT found in conf/modules.config and Nextflow scripts.
modules_config - FUSIONREPORT_DOWNLOAD found in conf/modules.config and Nextflow scripts.
modules_config - GATK4_BEDTOINTERVALLIST found in conf/modules.config and Nextflow scripts.
modules_config - GATK4_MARKDUPLICATES found in conf/modules.config and Nextflow scripts.
modules_config - GFFREAD found in conf/modules.config and Nextflow scripts.
modules_config - GTF_TO_REFFLAT found in conf/modules.config and Nextflow scripts.
modules_config - HGNC_DOWNLOAD found in conf/modules.config and Nextflow scripts.
modules_config - MULTIQC found in conf/modules.config and Nextflow scripts.
modules_config - PICARD_COLLECTRNASEQMETRICS found in conf/modules.config and Nextflow scripts.
modules_config - PICARD_COLLECTINSERTSIZEMETRICS found in conf/modules.config and Nextflow scripts.
modules_config - SALMON_INDEX found in conf/modules.config and Nextflow scripts.
modules_config - SALMON_QUANT found in conf/modules.config and Nextflow scripts.
modules_config - SAMTOOLS_FAIDX found in conf/modules.config and Nextflow scripts.
modules_config - SAMTOOLS_INDEX_FOR_ARRIBA found in conf/modules.config and Nextflow scripts.
modules_config - SAMTOOLS_SORT_FOR_ARRIBA found in conf/modules.config and Nextflow scripts.
modules_config - SAMTOOLS_VIEW_FOR_ARRIBA found in conf/modules.config and Nextflow scripts.
modules_config - SAMTOOLS_INDEX_FOR_STARFUSION found in conf/modules.config and Nextflow scripts.
modules_config - SAMTOOLS_INDEX_FOR_STARFUSION_CRAM found in conf/modules.config and Nextflow scripts.
modules_config - SAMTOOLS_VIEW_FOR_STARFUSION found in conf/modules.config and Nextflow scripts.
modules_config - STAR_FOR_ARRIBA found in conf/modules.config and Nextflow scripts.
modules_config - STAR_FOR_STARFUSION found in conf/modules.config and Nextflow scripts.
modules_config - STAR_GENOMEGENERATE found in conf/modules.config and Nextflow scripts.
modules_config - NFCORE_RNAFUSION found in conf/modules.config and Nextflow scripts.
modules_config - STARFUSION_DOWNLOAD found in conf/modules.config and Nextflow scripts.
modules_config - STRINGTIE_MERGE found in conf/modules.config and Nextflow scripts.
modules_config - VCF_COLLECT 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

Run details

nf-core/tools version 3.0.2
Run at 2024-12-20 14:40:43

…usion into refactor-references

nschcolnicov

@rannick Thank you very much for these amazing changes! Looks good to me!

atrigila

Looks good to me!! Thank you so much

rannick added 11 commits May 24, 2024 15:32

WIP: restructure reference building

3332ebb

refactor downloading of references

bf0c33e

fix params

a19abbd

fix

93fbfb8

update refs generation

b7dd137

fix small issues

89be7c1

Merge branch 'dev' of https://github.com/nf-core/rnafusion into refac…

d12312a

…tor-references

updates

0c6fe82

change strategy

eb6e354

intermediate state

40fbd83

ensembl to gencode, removing chrgtf

7a88971

rannick changed the base branch from master to dev November 12, 2024 12:00

rannick self-assigned this Nov 12, 2024

rannick added 4 commits November 13, 2024 10:03

syntax

0b1a067

merging

590b638

merging

f134b84

cleanup

7a5a917

rannick added 3 commits November 14, 2024 15:45

update modules, remove chrgtf, adapt with meta/no meta

d18b303

remove unnecessary file

786b9bf

add parameter interpretation in modules.config

460b645

rannick mentioned this pull request Nov 29, 2024

Asses if possible to connect build_reference and rnafusion workflows #553

Open

Merge branch 'dev' into refactor-references

0c90acb

rannick mentioned this pull request Nov 29, 2024

Make using COSMIC optional #547

Merged

10 tasks

rannick added 4 commits December 6, 2024 10:56

update fusioncatcher container

d290fcd

Merge branch 'refactor-references' of https://github.com/nf-core/rnaf…

19757b6

…usion into refactor-references

fix merge conflicts

1a1314e

fix linting issues

be6e102

rannick added 2 commits December 10, 2024 15:25

update GTF_TO_REFFLAT options, update snapshots

5409f8c

update star in snapshot

ef5ab96

atrigila mentioned this pull request Dec 10, 2024

Add nf-test to STARFUSION_BUILD and refactor module #583

Merged

10 tasks

rannick added 19 commits December 11, 2024 10:39

add human_gencode_filter to starfusion build

117884c

Merge branch 'dev' into refactor-references

4fab8b6

remove test.xml

3788788

Merge branch 'refactor-references' of https://github.com/nf-core/rnaf…

dcd9e21

…usion into refactor-references

update snap

8e9be7c

try updating snapshot again

5cdf95a

avoid using meta for remapping

fa128b6

fix merge conflicts

f2bc314

use custom container for fusioncatcher, fix typo

17ef233

fix merge conflicts

f3f5714

update changelog

f8dd516

update changelog, retrofit trim_workflowo

d62c4b5

fix merge conflicts

38de48b

add species as parameter

de5d6d5

fix some issues with channels

bdae293

add species to schema

509a792

fix erroneous addition of meta

8776835

Merge branch 'dev' into refactor-references

60f0da6

fixes

ab65540

rannick marked this pull request as ready for review December 20, 2024 13:03

rannick added the waiting-for-review label Dec 20, 2024

Merge branch 'dev' into refactor-references

31b400a

nschcolnicov approved these changes Dec 20, 2024

View reviewed changes

atrigila approved these changes Dec 20, 2024

View reviewed changes

rannick merged commit 31d29aa into dev Dec 20, 2024
7 checks passed

rannick deleted the refactor-references branch December 20, 2024 15:03

nschcolnicov mentioned this pull request Dec 26, 2024

Remove local module STARFUSION_DOWNLOAD #599

Merged

10 tasks

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Refactor references #505

Refactor references #505

rannick commented Oct 16, 2024 •

edited

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github-actions bot commented Oct 16, 2024 •

edited by nf-core-bot

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apeltzer commented Nov 7, 2024

github-actions bot commented Nov 13, 2024 •

edited

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❔ Tests ignored:

✅ Tests passed:

Run details

nschcolnicov left a comment

atrigila left a comment

Refactor references #505

Refactor references #505

Conversation

rannick commented Oct 16, 2024 • edited Loading

PR checklist

github-actions bot commented Oct 16, 2024 • edited by nf-core-bot Loading

apeltzer commented Nov 7, 2024

github-actions bot commented Nov 13, 2024 • edited Loading

nf-core pipelines lint overall result: Passed ✅

❔ Tests ignored:

✅ Tests passed:

Run details

nschcolnicov left a comment

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rannick commented Oct 16, 2024 •

edited

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github-actions bot commented Oct 16, 2024 •

edited by nf-core-bot

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github-actions bot commented Nov 13, 2024 •

edited

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