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64 lines
1.9 KiB
YAML
64 lines
1.9 KiB
YAML
name: trimgalore
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description: Trim FastQ files using Trim Galore!
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keywords:
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- trimming
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- adapters
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- sequencing adapters
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- fastq
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tools:
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- trimgalore:
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description: |
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A wrapper tool around Cutadapt and FastQC to consistently apply quality
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and adapter trimming to FastQ files, with some extra functionality for
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MspI-digested RRBS-type (Reduced Representation Bisufite-Seq) libraries.
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homepage: https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/
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documentation: https://github.com/FelixKrueger/TrimGalore/blob/master/Docs/Trim_Galore_User_Guide.md
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licence: ["GPL-3.0-or-later"]
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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: |
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List of input adapter trimmed FastQ files of size 1 and 2 for
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single-end and paired-end data, respectively.
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pattern: "*.{fq.gz}"
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- unpaired:
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type: file
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description: |
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FastQ files containing unpaired reads from read 1 or read 2
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pattern: "*unpaired*.fq.gz"
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- html:
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type: file
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description: FastQC report (optional)
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pattern: "*_{fastqc.html}"
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- zip:
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type: file
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description: FastQC report archive (optional)
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pattern: "*_{fastqc.zip}"
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- log:
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type: file
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description: Trim Galore! trimming report
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pattern: "*_{report.txt}"
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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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authors:
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- "@drpatelh"
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- "@ewels"
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- "@FelixKrueger"
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