nf-core_modules/software/fastqc/meta.yml

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name: FastQC
description: Run FastQC on sequenced reads
keywords:
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- Quality Control
- QC
- Adapters
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tools:
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- fastqc:
description: |
FastQC gives general quality metrics about your reads.
It provides information about the quality score distribution
across your reads, the per base sequence content (%A/C/G/T).
You get information about adapter contamination and other
overrepresented sequences.
homepage: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/
documentation: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/
params:
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- fastqc_args:
type: string
description: Additional command line arguments passed to fastqc.
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- out_dir:
type: string
description: |
The pipeline's output directory. By default, the module will
output files into `$out_dir/MODULE_NAME`
- publish_dir:
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type: string
description: |
Append to the path for the standard output directory provided by `$out_dir`.
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- publish_dir_mode:
type: string
description: |
Provide a value for the Nextflow `publishDir` mode parameter
(e.g. copy, link, ...)
- publish_results:
type: string
description: |
Whether or not to publish results into `publish_dir`. Set to `none` to not
publish any files at all; to `default` to publish all relevant files.
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input:
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- name:
type: string
description: Sample identifier
- single_end:
type: boolean
description: |
Boolean indicating whether the corresponding sample is single-end (true)
or paired-end (false).
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- reads:
type: file
description: |
List of input FastQ files of size 1 and 2 for single-end and paired-end data,
respectively.
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output:
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- report:
type: file
description: FastQC report
pattern: "*_fastqc.{zip,html}"
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authors:
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- "@grst"
- "@drpatelh"
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- "@ewels"
- "@FelixKrueger"