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7e8ad56688
* 1882 FASTP now supports interleaved FASTQ files Changes: - single_end FASTP pipes the FASTQ file - Using args, it can be configured for interleaved in `--interleaved_in` - Out is automatically interleaved if input is paired end. - Removed md5sum checks for FASTQ files as compression seemed to cause differences - Instead, we check inside the FASTQ files for content. Relates to #1882 Co-authored-by: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
68 lines
2.1 KiB
YAML
68 lines
2.1 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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licence: ["MIT"]
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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. Use 'single_end: true' to specify single ended or interleaved FASTQs. Use 'single_end: false' for paired-end reads.
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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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- save_trimmed_fail:
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type: boolean
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description: Specify true to save files that failed to pass trimming thresholds ending in `*.fail.fastq.gz`
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- save_merged:
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type: boolean
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description: Specify true to save all merged reads to the a file ending in `*.merged.fastq.gz`
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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/unmerged fastq reads
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pattern: "*fastp.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: "*.html"
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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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- versions:
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type: file
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description: File containing software versions
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pattern: "versions.yml"
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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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- reads_merged:
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type: file
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description: Reads that were successfully merged
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pattern: "*.{merged.fastq.gz}"
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authors:
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- "@drpatelh"
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- "@kevinmenden"
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