CI
1ebb61f1e8
Build pipeline: vsh-ci-dev-jsbwk
Source commit: 1e1ffb315f
Source message: Merge pull request #17 from viash-hub/add_biobox_modules
- Migrate a number of components to biobox
- Fix tests
- Reduce size of test resources
- Prepare for Viash Hub
119 lines
3.2 KiB
YAML
119 lines
3.2 KiB
YAML
name: "dupradar"
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info:
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migration_info:
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git_repo: https://github.com/nf-core/rnaseq.git
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paths: [modules/local/dupradar.nf]
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last_sha: 54721c6946daf6d602d7069dc127deef9cbe6b33
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description: |
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Assessment of duplication rates in RNA-Seq datasets
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argument_groups:
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- name: "Input"
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arguments:
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- name: "--id"
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type: string
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description: Sample ID
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- name: "--input"
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type: file
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required: true
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description: path to input alignment file in BAM format
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- name: "--gtf_annotation"
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type: file
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required: true
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description: path to GTF annotation file.
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- name: "--paired"
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type: boolean
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description: add flag if input alignment file consists of paired reads
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- name: "--strandedness"
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type: string
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required: false
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choices: ["forward", "reverse", "unstranded"]
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description: strandedness of input bam file reads (forward, reverse or unstranded (default, applicable to paired reads))
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- name: "Output"
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arguments:
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- name: "--output_dupmatrix"
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type: file
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direction: output
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required: false
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must_exist: true
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default: $id.dup_matrix.txt
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description: path to output file (txt) of duplicate tag counts
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- name: "--output_dup_intercept_mqc"
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type: file
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direction: output
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required: false
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must_exist: true
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default: $id.dup_intercept_mqc.txt
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description: path to output file (txt) of multiqc intercept value DupRadar
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- name: "--output_duprate_exp_boxplot"
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type: file
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direction: output
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required: false
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must_exist: true
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default: $id.duprate_exp_boxplot.pdf
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description: path to output file (pdf) of distribution of expression box plot
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- name: "--output_duprate_exp_densplot"
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type: file
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direction: output
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required: false
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must_exist: true
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default: $id.duprate_exp_densityplot.pdf
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description: path to output file (pdf) of 2D density scatter plot of duplicate tag counts
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- name: "--output_duprate_exp_denscurve_mqc"
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type: file
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direction: output
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required: false
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must_exist: true
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default: $id.duprate_exp_density_curve_mqc.txt
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description: path to output file (pdf) of density curve of gene duplication multiqc
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- name: "--output_expression_histogram"
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type: file
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direction: output
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required: false
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must_exist: true
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default: $id.expression_hist.pdf
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description: path to output file (pdf) of distribution of RPK values per gene histogram
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- name: "--output_intercept_slope"
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type: file
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direction: output
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required: false
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must_exist: true
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default: $id.intercept_slope.txt
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description: output file (txt) with progression of duplication rate value
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resources:
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- type: bash_script
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path: script.sh
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# Copied from https://github.com/nf-core/rnaseq/blob/3.12.0/bin/dupradar.r
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- path: dupradar.r
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test_resources:
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- type: bash_script
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path: test.sh
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- path: /testData/unit_test_resources/wgEncodeCaltechRnaSeqGm12878R1x75dAlignsRep2V2.bam
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- path: /testData/unit_test_resources/genes.gtf
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engines:
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- type: docker
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image: ubuntu:22.04
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setup:
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- type: apt
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packages: [ r-base ]
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- type: r
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bioc: [ dupRadar ]
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runners:
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- type: executable
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- type: nextflow
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