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sorelfitzgibbonsorelfitzgibbon
authoredMar 8, 2024
Merge pull request #36 from uclahs-cds/sfitz-rename-and-release
Rename pipeline and first release
2 parents e52143a + c27b24a commit f0ad5cd

7 files changed

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-33
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‎CHANGELOG.md

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@@ -8,6 +8,12 @@ This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.htm
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---
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## [Unreleased]
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### Added
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### Changed
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## [1.0.0-rc.1] - 2024-03-08
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### Added
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- Add `schema.yaml`
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- Add `template.config`
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- Add pipeline-Nextflow-module as submodule
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### Changed
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- Changed pipeline name `pipeline-SQC-DNA` to `pipeline-generate-SQC-BAM`
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- Use defaults for `CollectWgsMetrics` parameters
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- Pipeline name in output dir changed to `generate-SQC-BAM`
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- Changed `remove_duplicates` option to `samtools_remove_duplicates`

‎README.md

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# SQC-BAM
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# generate-SQC-BAM
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1. [Overview](#overview)
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2. [How To Run](#how-to-run)
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## Discussions
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- [Issue Tracker](https://github.com/uclahs-cds/pipeline-SQC-DNA/issues) to report errors and enhancement ideas.
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- Discussions can take place in [generate-SQC-BAM Discussions](https://github.com/uclahs-cds/pipeline-SQC-DNA/discussions)
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- [generate-SQC-BAM Pull Requests](https://github.com/uclahs-cds/pipeline-SQC-DNA/pulls) are also open for discussion
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- [Issue Tracker](https://github.com/uclahs-cds/pipeline-generate-SQC-BAM/issues) to report errors and enhancement ideas.
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- Discussions can take place in [generate-SQC-BAM Discussions](https://github.com/uclahs-cds/pipeline-generate-SQC-BAM/discussions)
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- [generate-SQC-BAM Pull Requests](https://github.com/uclahs-cds/pipeline-generate-SQC-BAM/pulls) are also open for discussion
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## Contributors
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Please see list of [Contributors](https://github.com/uclahs-cds/pipeline-SQC-DNA/graphs/contributors) at GitHub.
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Please see list of [Contributors](https://github.com/uclahs-cds/pipeline-generate-SQC-BAM/graphs/contributors) at GitHub.
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‎metadata.yaml

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---
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category: "pipeline"
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description: "Quality control analyses for sample level data"
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description: "Sample level Quality Control analyses for BAM files"
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maintainers: "Boutros Lab Infrastructure <BoutrosLabInfrastructure@mednet.ucla.edu>"
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languages: ["Nextflow", "Docker"]
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dependencies: ["Java", "Nextflow", "Docker"]

‎nextflow.config

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name = 'generate-SQC-BAM'
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author = 'Sorel Fitz-Gibbon'
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description = 'Sample level QC for DNA sequencing data'
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version = '0.0.1'
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version = '1.0.0-rc.1'
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}

‎nftest.yml

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@@ -15,22 +15,22 @@ cases:
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verbose: true
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asserts:
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- actual: generate-SQC-BAM-*/TWGSAMIN000001/SAMtools-*/output/SAMtools-*_TWGSAMIN_HG002.N_stats.txt
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expect: /hot/software/pipeline/pipeline-SQC-DNA/Nextflow/development/test-output/SAMtools-1.18_TWGSAMIN_HG002.N_stats.txt
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expect: /hot/software/pipeline/pipeline-generate-SQC-BAM/Nextflow/development/test-output/SAMtools-1.18_TWGSAMIN_HG002.N_stats.txt
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method: md5
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- actual: generate-SQC-BAM-*/TWGSAMIN000001/SAMtools-*/output/SAMtools-*_TWGSAMIN_S2-v1.1.5_stats.txt
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expect: /hot/software/pipeline/pipeline-SQC-DNA/Nextflow/development/test-output/SAMtools-1.18_TWGSAMIN_S2-v1.1.5_stats.txt
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expect: /hot/software/pipeline/pipeline-generate-SQC-BAM/Nextflow/development/test-output/SAMtools-1.18_TWGSAMIN_S2-v1.1.5_stats.txt
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method: md5
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- actual: generate-SQC-BAM-*/TWGSAMIN000001/Picard-*/output/Picard-*_TWGSAMIN_HG002.N_wgs-metrics.txt
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expect: /hot/software/pipeline/pipeline-SQC-DNA/Nextflow/development/test-output/Picard-3.1.0_TWGSAMIN_HG002.N_wgs-metrics.txt
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expect: /hot/software/pipeline/pipeline-generate-SQC-BAM/Nextflow/development/test-output/Picard-3.1.0_TWGSAMIN_HG002.N_wgs-metrics.txt
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script: test/assert_txt.sh
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- actual: generate-SQC-BAM-*/TWGSAMIN000001/Picard-*/output/Picard-*_TWGSAMIN_S2-v1.1.5_wgs-metrics.txt
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expect: /hot/software/pipeline/pipeline-SQC-DNA/Nextflow/development/test-output/Picard-3.1.0_TWGSAMIN_S2-v1.1.5_wgs-metrics.txt
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expect: /hot/software/pipeline/pipeline-generate-SQC-BAM/Nextflow/development/test-output/Picard-3.1.0_TWGSAMIN_S2-v1.1.5_wgs-metrics.txt
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script: test/assert_txt.sh
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- actual: generate-SQC-BAM-*/TWGSAMIN000001/Qualimap-*/output/Qualimap-*_TWGSAMIN_HG002.N_stats/genome_results.txt
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expect: /hot/software/pipeline/pipeline-SQC-DNA/Nextflow/development/test-output/Qualimap-2.3_TWGSAMIN_HG002.N_stats/genome_results.txt
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expect: /hot/software/pipeline/pipeline-generate-SQC-BAM/Nextflow/development/test-output/Qualimap-2.3_TWGSAMIN_HG002.N_stats/genome_results.txt
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method: md5
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- actual: generate-SQC-BAM-*/TWGSAMIN000001/Qualimap-*/output/Qualimap-*_TWGSAMIN_S2-v1.1.5_stats/genome_results.txt
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expect: /hot/software/pipeline/pipeline-SQC-DNA/Nextflow/development/test-output/Qualimap-2.3_TWGSAMIN_S2-v1.1.5_stats/genome_results.txt
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expect: /hot/software/pipeline/pipeline-generate-SQC-BAM/Nextflow/development/test-output/Qualimap-2.3_TWGSAMIN_S2-v1.1.5_stats/genome_results.txt
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method: md5
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- name: a_mini-all-tools-multiple-samples
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message: test all tools with 1 normal and 2 tumor samples
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verbose: true
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asserts:
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- actual: generate-SQC-BAM-*/TWGSAMIN000001/SAMtools-*/output/SAMtools-*_TWGSAMIN_HG002.N_stats.txt
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expect: /hot/software/pipeline/pipeline-SQC-DNA/Nextflow/development/test-output/SAMtools-1.18_TWGSAMIN_HG002.N_stats.txt
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expect: /hot/software/pipeline/pipeline-generate-SQC-BAM/Nextflow/development/test-output/SAMtools-1.18_TWGSAMIN_HG002.N_stats.txt
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method: md5
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- actual: generate-SQC-BAM-*/TWGSAMIN000001/SAMtools-*/output/SAMtools-*_TWGSAMIN_S2-v1.1.5_stats.txt
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expect: /hot/software/pipeline/pipeline-SQC-DNA/Nextflow/development/test-output/SAMtools-1.18_TWGSAMIN_S2-v1.1.5_stats.txt
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expect: /hot/software/pipeline/pipeline-generate-SQC-BAM/Nextflow/development/test-output/SAMtools-1.18_TWGSAMIN_S2-v1.1.5_stats.txt
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method: md5
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- actual: generate-SQC-BAM-*/TWGSAMIN000001/SAMtools-*/output/SAMtools-*_TWGSAMIN_S2-v1.1.5.n1_stats.txt
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expect: /hot/software/pipeline/pipeline-SQC-DNA/Nextflow/development/test-output/SAMtools-1.18_TWGSAMIN_S2-v1.1.5.n1_stats.txt
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expect: /hot/software/pipeline/pipeline-generate-SQC-BAM/Nextflow/development/test-output/SAMtools-1.18_TWGSAMIN_S2-v1.1.5.n1_stats.txt
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method: md5
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- actual: generate-SQC-BAM-*/TWGSAMIN000001/Picard-*/output/Picard-*_TWGSAMIN_HG002.N_wgs-metrics.txt
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expect: /hot/software/pipeline/pipeline-SQC-DNA/Nextflow/development/test-output/Picard-3.1.0_TWGSAMIN_HG002.N_wgs-metrics.txt
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expect: /hot/software/pipeline/pipeline-generate-SQC-BAM/Nextflow/development/test-output/Picard-3.1.0_TWGSAMIN_HG002.N_wgs-metrics.txt
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script: test/assert_txt.sh
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- actual: generate-SQC-BAM-*/TWGSAMIN000001/Picard-*/output/Picard-*_TWGSAMIN_S2-v1.1.5_wgs-metrics.txt
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expect: /hot/software/pipeline/pipeline-SQC-DNA/Nextflow/development/test-output/Picard-3.1.0_TWGSAMIN_S2-v1.1.5_wgs-metrics.txt
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expect: /hot/software/pipeline/pipeline-generate-SQC-BAM/Nextflow/development/test-output/Picard-3.1.0_TWGSAMIN_S2-v1.1.5_wgs-metrics.txt
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script: test/assert_txt.sh
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- actual: generate-SQC-BAM-*/TWGSAMIN000001/Picard-*/output/Picard-*_TWGSAMIN_S2-v1.1.5.n1_wgs-metrics.txt
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expect: /hot/software/pipeline/pipeline-SQC-DNA/Nextflow/development/test-output/Picard-3.1.0_TWGSAMIN_S2-v1.1.5.n1_wgs-metrics.txt
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expect: /hot/software/pipeline/pipeline-generate-SQC-BAM/Nextflow/development/test-output/Picard-3.1.0_TWGSAMIN_S2-v1.1.5.n1_wgs-metrics.txt
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script: test/assert_txt.sh
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- actual: generate-SQC-BAM-*/TWGSAMIN000001/Qualimap-*/output/Qualimap-*_TWGSAMIN_HG002.N_stats/genome_results.txt
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expect: /hot/software/pipeline/pipeline-SQC-DNA/Nextflow/development/test-output/Qualimap-2.3_TWGSAMIN_HG002.N_stats/genome_results.txt
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expect: /hot/software/pipeline/pipeline-generate-SQC-BAM/Nextflow/development/test-output/Qualimap-2.3_TWGSAMIN_HG002.N_stats/genome_results.txt
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method: md5
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- actual: generate-SQC-BAM-*/TWGSAMIN000001/Qualimap-*/output/Qualimap-*_TWGSAMIN_S2-v1.1.5_stats/genome_results.txt
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expect: /hot/software/pipeline/pipeline-SQC-DNA/Nextflow/development/test-output/Qualimap-2.3_TWGSAMIN_S2-v1.1.5_stats/genome_results.txt
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expect: /hot/software/pipeline/pipeline-generate-SQC-BAM/Nextflow/development/test-output/Qualimap-2.3_TWGSAMIN_S2-v1.1.5_stats/genome_results.txt
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method: md5
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- actual: generate-SQC-BAM-*/TWGSAMIN000001/Qualimap-*/output/Qualimap-*_TWGSAMIN_S2-v1.1.5.n1_stats/genome_results.txt
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expect: /hot/software/pipeline/pipeline-SQC-DNA/Nextflow/development/test-output/Qualimap-2.3_TWGSAMIN_S2-v1.1.5.n1_stats/genome_results.txt
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expect: /hot/software/pipeline/pipeline-generate-SQC-BAM/Nextflow/development/test-output/Qualimap-2.3_TWGSAMIN_S2-v1.1.5.n1_stats/genome_results.txt
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method: md5
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- name: a_mini-stats
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message: test samtools stats
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verbose: true
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asserts:
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- actual: generate-SQC-BAM-*/TWGSAMIN000001/SAMtools-*/output/SAMtools-*_TWGSAMIN_HG002.N_stats.txt
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expect: /hot/software/pipeline/pipeline-SQC-DNA/Nextflow/development/test-output/SAMtools-1.18_TWGSAMIN_HG002.N_stats.txt
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expect: /hot/software/pipeline/pipeline-generate-SQC-BAM/Nextflow/development/test-output/SAMtools-1.18_TWGSAMIN_HG002.N_stats.txt
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method: md5
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- actual: generate-SQC-BAM-*/TWGSAMIN000001/SAMtools-*/output/SAMtools-*_TWGSAMIN_S2-v1.1.5_stats.txt
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expect: /hot/software/pipeline/pipeline-SQC-DNA/Nextflow/development/test-output/SAMtools-1.18_TWGSAMIN_S2-v1.1.5_stats.txt
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expect: /hot/software/pipeline/pipeline-generate-SQC-BAM/Nextflow/development/test-output/SAMtools-1.18_TWGSAMIN_S2-v1.1.5_stats.txt
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method: md5
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- name: a_mini-collectwgsmetrics
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message: test collectwgsmetrics
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verbose: true
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asserts:
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- actual: generate-SQC-BAM-*/TWGSAMIN000001/Picard-*/output/Picard-*_TWGSAMIN_HG002.N_wgs-metrics.txt
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expect: /hot/software/pipeline/pipeline-SQC-DNA/Nextflow/development/test-output/Picard-3.1.0_TWGSAMIN_HG002.N_wgs-metrics.txt
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expect: /hot/software/pipeline/pipeline-generate-SQC-BAM/Nextflow/development/test-output/Picard-3.1.0_TWGSAMIN_HG002.N_wgs-metrics.txt
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script: test/assert_txt.sh
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- actual: generate-SQC-BAM-*/TWGSAMIN000001/Picard-*/output/Picard-*_TWGSAMIN_S2-v1.1.5_wgs-metrics.txt
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expect: /hot/software/pipeline/pipeline-SQC-DNA/Nextflow/development/test-output/Picard-3.1.0_TWGSAMIN_S2-v1.1.5_wgs-metrics.txt
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expect: /hot/software/pipeline/pipeline-generate-SQC-BAM/Nextflow/development/test-output/Picard-3.1.0_TWGSAMIN_S2-v1.1.5_wgs-metrics.txt
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script: test/assert_txt.sh
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- name: a_mini-bamqc
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message: test bamqc
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verbose: true
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asserts:
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- actual: generate-SQC-BAM-*/TWGSAMIN000001/Qualimap-*/output/Qualimap-*_TWGSAMIN_HG002.N_stats/genome_results.txt
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expect: /hot/software/pipeline/pipeline-SQC-DNA/Nextflow/development/test-output/Qualimap-2.3_TWGSAMIN_HG002.N_stats/genome_results.txt
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expect: /hot/software/pipeline/pipeline-generate-SQC-BAM/Nextflow/development/test-output/Qualimap-2.3_TWGSAMIN_HG002.N_stats/genome_results.txt
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method: md5
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- actual: generate-SQC-BAM-*/TWGSAMIN000001/Qualimap-*/output/Qualimap-*_TWGSAMIN_S2-v1.1.5_stats/genome_results.txt
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expect: /hot/software/pipeline/pipeline-SQC-DNA/Nextflow/development/test-output/Qualimap-2.3_TWGSAMIN_S2-v1.1.5_stats/genome_results.txt
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expect: /hot/software/pipeline/pipeline-generate-SQC-BAM/Nextflow/development/test-output/Qualimap-2.3_TWGSAMIN_S2-v1.1.5_stats/genome_results.txt
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method: md5

‎test/yaml/a_mini-multiple-samples.yaml

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dataset_id: 'TWGSAMIN'
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input:
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normal:
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- path: /hot/software/pipeline/pipeline-SQC-DNA/Nextflow/development/test-input/HG002.N-n2.bam
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- path: /hot/software/pipeline/pipeline-generate-SQC-BAM/Nextflow/development/test-input/HG002.N-n2.bam
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read_length: 150
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tumor:
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- path: /hot/software/pipeline/pipeline-SQC-DNA/Nextflow/development/test-input/S2.T-n2.bam
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- path: /hot/software/pipeline/pipeline-generate-SQC-BAM/Nextflow/development/test-input/S2.T-n2.bam
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read_length: 150
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- path: /hot/software/pipeline/pipeline-SQC-DNA/Nextflow/development/test-input/S2.T-n1_SMadjust.bam
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- path: /hot/software/pipeline/pipeline-generate-SQC-BAM/Nextflow/development/test-input/S2.T-n1_SMadjust.bam
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read_length: 150

‎test/yaml/a_mini.yaml

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dataset_id: 'TWGSAMIN'
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input:
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normal:
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- path: /hot/software/pipeline/pipeline-SQC-DNA/Nextflow/development/test-input/HG002.N-n2.bam
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- path: /hot/software/pipeline/pipeline-generate-SQC-BAM/Nextflow/development/test-input/HG002.N-n2.bam
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read_length: 150
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tumor:
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- path: /hot/software/pipeline/pipeline-SQC-DNA/Nextflow/development/test-input/S2.T-n2.bam
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- path: /hot/software/pipeline/pipeline-generate-SQC-BAM/Nextflow/development/test-input/S2.T-n2.bam
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read_length: 150

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