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e745e167c1
* fix yml formatting * allow fastq.gz and fq.gz as file input, add meta.yml and test * fix yaml files * Revert "allow fastq.gz and fq.gz as file input, add meta.yml and test" This reverts commit 34002d7a7a8c7f7bb4600c3377f35c87849f71a4. * prettier magic! * fix comments for yamllint * remove node version number * fix linting errors Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
62 lines
1.7 KiB
YAML
62 lines
1.7 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
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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/unmerged 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: "*.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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