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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
57 lines
1.5 KiB
YAML
57 lines
1.5 KiB
YAML
name: fastp
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description: Perform adapter/quality trimming on sequencing reads
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keywords:
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- trimming
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- quality control
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- fastq
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tools:
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- fastp:
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description: |
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A tool designed to provide fast all-in-one preprocessing for FastQ files. This tool is developed in C++ with multithreading supported to afford high performance.
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documentation: https://github.com/OpenGene/fastp
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doi: https://doi.org/10.1093/bioinformatics/bty560
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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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- reads:
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type: file
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description: |
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List of input FastQ files of size 1 and 2 for single-end and paired-end data,
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respectively.
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output:
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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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- reads:
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type: file
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description: The trimmed/modified fastq reads
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pattern: "*trim.fastq.gz"
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- json:
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type: file
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description: Results in JSON format
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pattern: "*.json"
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- html:
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type: file
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description: Results in HTML format
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pattern: "*.thml"
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- log:
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type: file
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description: fastq log file
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pattern: "*.log"
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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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- reads_fail:
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type: file
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description: Reads the failed the preprocessing
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pattern: "*fail.fastq.gz"
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authors:
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- "@drpatelh"
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- "@kevinmenden"
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