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e745e167c1
* fix yml formatting * allow fastq.gz and fq.gz as file input, add meta.yml and test * fix yaml files * Revert "allow fastq.gz and fq.gz as file input, add meta.yml and test" This reverts commit 34002d7a7a8c7f7bb4600c3377f35c87849f71a4. * prettier magic! * fix comments for yamllint * remove node version number * fix linting errors Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
52 lines
1.4 KiB
YAML
52 lines
1.4 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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- fastq
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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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licence: ["GPL-2.0-only"]
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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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- html:
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type: file
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description: FastQC report
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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
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pattern: "*_{fastqc.zip}"
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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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- "@grst"
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- "@ewels"
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- "@FelixKrueger"
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