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99 lines
3.4 KiB
YAML
99 lines
3.4 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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params:
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- outdir:
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type: string
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description: |
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The pipeline's output directory. By default, the module will
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output files into `$params.outdir/<SOFTWARE>`
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- publish_dir_mode:
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type: string
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description: |
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Value for the Nextflow `publishDir` mode parameter.
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Available: symlink, rellink, link, copy, copyNoFollow, move.
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- enable_conda:
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type: boolean
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description: |
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Run the module with Conda using the software specified
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via the `conda` directive
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- singularity_pull_docker_container:
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type: boolean
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description: |
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Instead of directly downloading Singularity images for use with Singularity,
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force the workflow to pull and convert Docker containers instead.
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- clip_r1:
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type: integer
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description: |
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Instructs Trim Galore to remove bp from the 5' end of read 1
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(or single-end reads)
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- clip_r2:
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type: integer
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description: |
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Instructs Trim Galore to remove bp from the 5' end of read 2
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(paired-end reads only)
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- three_prime_clip_r1:
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type: integer
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description: |
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Instructs Trim Galore to remove bp from the 3' end of read 1
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AFTER adapter/quality trimming has been performed
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- three_prime_clip_r2:
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type: integer
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description: |
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Instructs Trim Galore to re move bp from the 3' end of read 2
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AFTER adapter/quality trimming has been performed
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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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- 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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- 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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- "@ewels"
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- "@FelixKrueger"
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