nf-core_modules/software/fastqc/meta.yml

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name: fastqc
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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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- outdir:
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type: string
description: |
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:
type: string
description: |
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Value for the Nextflow `publishDir` mode parameter.
Available: symlink, rellink, link, copy, copyNoFollow, move.
- conda:
type: boolean
description: |
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Run the module with Conda using the software specified
via the `conda` directive
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input:
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- meta:
type: map
description: |
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Groovy Map containing sample information
e.g. [ id:'test', single_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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- options:
type: map
description: |
Groovy Map containing module options for passing command-line arguments and
output file paths.
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output:
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- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- html:
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type: file
description: FastQC report
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pattern: "*_fastqc.html"
- zip:
type: file
description: FastQC report archive
pattern: "*_fastqc.zip"
- version:
type: file
description: File containing software version
pattern: "*.version.txt"
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authors:
- "@drpatelh"
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- "@grst"
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- "@ewels"
- "@FelixKrueger"