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63 lines
1.9 KiB
YAML
63 lines
1.9 KiB
YAML
name: FastQC
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description: Run FastQC on sequenced reads
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keywords:
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- Quality Control
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- QC
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- Adapters
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tools:
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- fastqc:
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description: |
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FastQC gives general quality metrics about your reads.
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It provides information about the quality score distribution
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across your reads, the per base sequence content (%A/C/G/T).
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You get information about adapter contamination and other
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overrepresented sequences.
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homepage: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/
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documentation: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/
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params:
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- fastqc_args:
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type: string
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description: Additional command line arguments passed to fastqc.
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- out_dir:
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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 `$out_dir/MODULE_NAME`
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- publish_dir:
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type: string
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description: |
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Append to the path for the standard output directory provided by `$out_dir`.
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- publish_dir_mode:
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type: string
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description: |
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Provide a value for the Nextflow `publishDir` mode parameter
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(e.g. copy, link, ...)
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- publish_results:
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type: string
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description: |
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Whether or not to publish results into `publish_dir`. Set to `none` to not
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publish any files at all; to `default` to publish all relevant files.
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input:
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- name:
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type: string
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description: Sample identifier
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- single_end:
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type: boolean
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description: |
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Boolean indicating whether the corresponding sample is single-end (true)
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or paired-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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- report:
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type: file
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description: FastQC report
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pattern: "*_fastqc.{zip,html}"
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authors:
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- "@grst"
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- "@drpatelh"
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- "@ewels"
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- "@FelixKrueger"
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