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* Update README * Rename pytest_software.yml to pytest_modules.yml * Rename main software directory to modules * Remove deprecated modules * Rename tests software to modules * Replace paths for tests in pytest_modules.yml * Replace software with modules in Github Actions * Replace software with modules in main.nf tests * Rename software to modules in test.yml
51 lines
1.4 KiB
YAML
51 lines
1.4 KiB
YAML
name: rseqc_readduplication
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description: Calculate read duplication rate
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keywords:
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- rnaseq
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- duplication
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tools:
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- rseqc:
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description: |
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RSeQC package provides a number of useful modules that can comprehensively evaluate
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high throughput sequence data especially RNA-seq data.
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homepage: http://rseqc.sourceforge.net/
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documentation: http://rseqc.sourceforge.net/
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doi: 10.1093/bioinformatics/bts356
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input:
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- meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test', single_end:false ]
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- bam:
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type: file
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description: the alignment in bam format
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pattern: "*.{bam}"
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- bed:
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type: file
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description: a bed file for the reference gene model
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pattern: "*.{bed}"
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output:
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- seq_xls:
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type: file
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description: Read duplication rate determined from mapping position of read
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pattern: "*seq.DupRate.xls"
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- pos_xls:
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type: file
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description: Read duplication rate determined from sequence of read
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pattern: "*pos.DupRate.xls"
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- pdf:
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type: file
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description: plot of duplication rate
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pattern: "*.pdf"
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- rscript:
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type: file
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description: script to reproduce the plot
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pattern: "*.R"
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- version:
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type: file
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description: File containing software version
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pattern: "*.{version.txt}"
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authors:
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- "@drpatelh"
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- "@kevinmenden"
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