add chromograph #366

ramprasadn · 2023-06-26T14:18:30Z

PR checklist

This PR adds chromograph to visualize the output from upd module.

github-actions · 2023-06-26T14:21:28Z

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

Posted for pipeline commit 3467911

+| ✅ 156 tests passed       |+
#| ❔   3 tests were ignored |#
!| ❗   2 tests had warnings |!

❗ Test warnings:

pipeline_todos - TODO string in README.md: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file.
pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required

❔ Tests ignored:

files_exist - File is ignored: conf/modules.config
files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
files_unchanged - File ignored due to lint config: .github/workflows/linting.yml

✅ Tests passed:

files_exist - File found: .gitattributes
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nextflow_config - Config variable found: manifest.name
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nextflow_config - Config variable found: params.schema_ignore_params
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 !>=
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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
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/workflows/branch.yml matches the template
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files_unchanged - assets/email_template.html matches the template
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files_unchanged - assets/sendmail_template.txt matches the template
files_unchanged - assets/nf-core-raredisease_logo_light.png matches the template
files_unchanged - docs/images/nf-core-raredisease_logo_light.png matches the template
files_unchanged - docs/images/nf-core-raredisease_logo_dark.png matches the template
files_unchanged - docs/README.md matches the template
files_unchanged - lib/nfcore_external_java_deps.jar matches the template
files_unchanged - lib/NfcoreSchema.groovy 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: 22.10.1, Config: 22.10.1
readme - README Zenodo placeholder was replaced with DOI.
pipeline_name_conventions - Name adheres to nf-core convention
template_strings - Did not find any Jinja template strings (303 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: clean-up.yml
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: branch.yml
actions_schema_validation - Workflow validation passed: awsfulltest.yml
actions_schema_validation - Workflow validation passed: fix-linting.yml
actions_schema_validation - Workflow validation passed: awstest.yml
actions_schema_validation - Workflow validation passed: linting_comment.yml
actions_schema_validation - Workflow validation passed: ci.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' 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'

Run details

nf-core/tools version 2.8
Run at 2023-06-26 17:35:09

Lucpen · 2023-06-27T07:06:47Z

CHANGELOG.md

+- Add `public_aws_ecr` profile for using AWS ECR public gallery images [#360](https://github.com/nf-core/raredisease/pull/360)
+- GATK's ShiftFasta to generate all the files required for mitochondrial analysis [#354](https://github.com/nf-core/raredisease/pull/354)
+- Feature to calculate CADD scores for indels [#325](https://github.com/nf-core/raredisease/pull/325)
+- HmtNote to annotate mitochondria [#355](https://github.com/nf-core/raredisease/pull/355)
+- MT del script to detect mitochondrial deletions [#349](https://github.com/nf-core/raredisease/pull/349)
+- eKLIPse to identify large mitochondrial deletions [#365](https://github.com/nf-core/raredisease/pull/365)
+- UPD+Chromograph to identify and visualize UPD sites and regions in the chromosomes [#364](https://github.com/nf-core/raredisease/pull/364) and [#366](https://github.com/nf-core/raredisease/pull/366)


Thanks for adding the MT ones! :)

ramprasadn added 2 commits June 26, 2023 16:16

add chromograph [skip ci]

cfb6edb

Merge branch 'dev' into chromograph

43b27b9

ramprasadn changed the title ~~add chromograph [skip ci]~~ add chromograph Jun 26, 2023

update chromograph

3d8227a

ramprasadn marked this pull request as ready for review June 26, 2023 16:47

ramprasadn added 3 commits June 26, 2023 19:16

update readme and output

7483d7e

update changelog

8dc606b

update readme

3467911

ramprasadn requested review from Lucpen and jemten June 26, 2023 17:47

Lucpen approved these changes Jun 27, 2023

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Lucpen reviewed Jun 27, 2023

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ramprasadn merged commit a39e1d8 into nf-core:dev Jun 27, 2023

ramprasadn deleted the chromograph branch June 27, 2023 07:30

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nf-core lint overall result: Passed ✅ ⚠️

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ramprasadn commented Jun 26, 2023 •

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