Annotate SVs #408

fellen31 · 2024-10-04T12:00:19Z

PR checklist

github-actions · 2024-10-04T12:02:48Z

`nf-core lint` overall result: Passed ✅

Posted for pipeline commit f97d4a6

+| ✅ 170 tests passed       |+
#| ❔  20 tests were ignored |#

❔ Tests ignored:

files_exist - File is ignored: CODE_OF_CONDUCT.md
files_exist - File is ignored: assets/nf-core-nallo_logo_light.png
files_exist - File is ignored: docs/README.md
files_exist - File is ignored: docs/images/nf-core-nallo_logo_light.png
files_exist - File is ignored: docs/images/nf-core-nallo_logo_dark.png
files_exist - File is ignored: .github/ISSUE_TEMPLATE/config.yml
files_exist - File is ignored: .github/workflows/awstest.yml
files_exist - File is ignored: .github/workflows/awsfulltest.yml
files_exist - File is ignored: conf/modules.config
nextflow_config - Config variable ignored: manifest.name
nextflow_config - Config variable ignored: manifest.homePage
files_unchanged - File ignored due to lint config: CODE_OF_CONDUCT.md
files_unchanged - File ignored due to lint config: .github/CONTRIBUTING.md
files_unchanged - File ignored due to lint config: .github/ISSUE_TEMPLATE/bug_report.yml
files_unchanged - File ignored due to lint config: assets/nf-core-nallo_logo_light.png
files_unchanged - File ignored due to lint config: docs/images/nf-core-nallo_logo_light.png
files_unchanged - File ignored due to lint config: docs/images/nf-core-nallo_logo_dark.png
files_unchanged - File ignored due to lint config: docs/README.md
files_unchanged - File ignored due to lint config: .gitignore or .prettierignore
modules_config - modules_config

✅ 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: 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/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: conf/test.config
files_exist - File found: conf/test_full.config
files_exist - File found: docs/output.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: 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-nallo_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/WorkflowNallo.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.nextflowVersion
nextflow_config - Config variable found: manifest.description
nextflow_config - Config variable found: manifest.version
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 dag.file ended with .html
nextflow_config - Config variable manifest.nextflowVersion started with >= or !>=
nextflow_config - Config manifest.version ends in dev: 0.4.0dev
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.skip_qc= false
nextflow_config - Config default value correct: params.skip_short_variant_calling= false
nextflow_config - Config default value correct: params.skip_assembly_wf= false
nextflow_config - Config default value correct: params.skip_mapping_wf= false
nextflow_config - Config default value correct: params.skip_methylation_wf= false
nextflow_config - Config default value correct: params.skip_repeat_calling= false
nextflow_config - Config default value correct: params.skip_repeat_annotation= false
nextflow_config - Config default value correct: params.skip_phasing_wf= false
nextflow_config - Config default value correct: params.skip_snv_annotation= false
nextflow_config - Config default value correct: params.skip_sv_annotation= false
nextflow_config - Config default value correct: params.skip_cnv_calling= false
nextflow_config - Config default value correct: params.skip_call_paralogs= false
nextflow_config - Config default value correct: params.skip_rank_variants= false
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.preset= revio
nextflow_config - Config default value correct: params.variant_caller= deepvariant
nextflow_config - Config default value correct: params.sv_caller= severus
nextflow_config - Config default value correct: params.phaser= longphase
nextflow_config - Config default value correct: params.hifiasm_mode= hifi-only
nextflow_config - Config default value correct: params.parallel_alignments= 1
nextflow_config - Config default value correct: params.parallel_snv= 13
nextflow_config - Config default value correct: params.vep_cache_version= 110
nextflow_config - Config default value correct: params.deepvariant_model_type= PACBIO
nextflow_config - Config default value correct: params.pipelines_testdata_base_path= https://raw.githubusercontent.com/genomic-medicine-sweden/test-datasets/7be7114cb132be8cae9343f225bcf42ec11ecc1b/
files_unchanged - .gitattributes matches the template
files_unchanged - .prettierrc.yml matches the template
files_unchanged - LICENSE matches the template
files_unchanged - .github/.dockstore.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
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
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 (574 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: ci.yml
actions_schema_validation - Workflow validation passed: linting_comment.yml
actions_schema_validation - Workflow validation passed: ci_master.yml
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: download_pipeline.yml
actions_schema_validation - Workflow validation passed: awstest.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: branch.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.
base_config - HIFIASM found in conf/base.config and Nextflow scripts.
base_config - SAMTOOLS_MERGE found in conf/base.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 2024-10-08 07:12:15

fellen31 · 2024-10-07T12:47:02Z

Oops, missing docs.

fellen31 · 2024-10-09T11:06:13Z

~~Probably blocked by nextflow-io/nf-schema#55 after template update.~~

Use for second copy: https://github.com/nf-core/hgtseq/blob/683daaf41bb396839445e603152b45daa141ced4/workflows/hgtseq.nf#L259-L310

And vep with --regulatory should be ok with 110.

fellen31 · 2024-10-11T07:44:43Z

This PR should now be ready for review 😅

I think --regulatory should be fine with vep 110, and the SVDB csv was not using fromSamplesheet anyway.

jemten

Nice work!

jemten · 2024-10-11T08:41:01Z

modules/nf-core/svdb/build/main.nf

I can't see this module being used anywhere. Remove?

Yep, I decided not to have it.

jemten · 2024-10-11T08:42:27Z

subworkflows/local/annotate_svs/main.nf

+        ch_svdb_in.out_frqs.toList(),
+        ch_svdb_in.vcf_dbs.toList(),
+        []
+    )


add the SVDB version to ch_versions

jemten

Looks good to me

fellen31 force-pushed the annotate-svs branch 2 times, most recently from 299f76f to f19c2a1 Compare October 4, 2024 12:01

fellen31 force-pushed the annotate-svs branch 2 times, most recently from 706dea2 to f870e9e Compare October 4, 2024 12:08

This was linked to issues Oct 4, 2024

Add SVDB QUERY #383

Closed

Add VEP for SVs #384

Closed

fellen31 force-pushed the annotate-svs branch 6 times, most recently from e003469 to 4007212 Compare October 7, 2024 12:08

fellen31 marked this pull request as ready for review October 7, 2024 12:45

fellen31 requested a review from a team as a code owner October 7, 2024 12:45

fellen31 linked an issue Oct 7, 2024 that may be closed by this pull request

Implement nf-test for annotate_structural_variants #282

Closed

fellen31 marked this pull request as draft October 7, 2024 12:46

fellen31 force-pushed the annotate-svs branch from dd70ab3 to d3a25c2 Compare October 7, 2024 16:34

fellen31 marked this pull request as ready for review October 8, 2024 07:07

fellen31 force-pushed the annotate-svs branch from 51bc2cc to f97d4a6 Compare October 8, 2024 07:10

fellen31 marked this pull request as draft October 9, 2024 12:46

fellen31 and others added 5 commits October 11, 2024 07:07

wip

308d147

working

18ab1c0

fix snv annotation

afd110d

docs and split

a8207e2

update docs

00f48d2

fellen31 force-pushed the annotate-svs branch 2 times, most recently from 7f76060 to eaf91b7 Compare October 11, 2024 05:22

fellen31 force-pushed the annotate-svs branch 2 times, most recently from d0d6049 to 6f8ef42 Compare October 11, 2024 07:22

add back regulatory

402f276

fellen31 force-pushed the annotate-svs branch from 6f8ef42 to 402f276 Compare October 11, 2024 07:25

fellen31 marked this pull request as ready for review October 11, 2024 07:43

jemten reviewed Oct 11, 2024

View reviewed changes

fellen31 added 2 commits October 11, 2024 10:48

review suggestions

cda8f37

prettier

6b518cb

fellen31 mentioned this pull request Oct 11, 2024

Update metro map #423

Merged

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jemten approved these changes Oct 11, 2024

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fellen31 merged commit 777cd7b into genomic-medicine-sweden:dev Oct 14, 2024
16 checks passed

fellen31 deleted the annotate-svs branch October 14, 2024 07:15

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Annotate SVs #408

Annotate SVs #408

fellen31 commented Oct 4, 2024 •

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github-actions bot commented Oct 4, 2024 •

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❔ Tests ignored:

✅ Tests passed:

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fellen31 commented Oct 7, 2024

fellen31 commented Oct 9, 2024 •

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fellen31 commented Oct 11, 2024

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Annotate SVs #408

Annotate SVs #408

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fellen31 commented Oct 4, 2024 • edited Loading

PR checklist

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nf-core lint overall result: Passed ✅

❔ Tests ignored:

✅ Tests passed:

Run details

fellen31 commented Oct 7, 2024

fellen31 commented Oct 9, 2024 • edited Loading

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fellen31 commented Oct 4, 2024 •

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`nf-core lint` overall result: Passed ✅

fellen31 commented Oct 9, 2024 •

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