2020-08-06 23:50:49 +00:00
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name: fastqc
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2019-12-05 14:18:09 +00:00
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description: Run FastQC on sequenced reads
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keywords:
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2020-08-07 14:05:25 +00:00
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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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2019-12-05 14:18:09 +00:00
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tools:
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2020-08-07 14:05:25 +00:00
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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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2020-07-15 08:16:48 +00:00
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params:
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2020-08-07 14:05:25 +00:00
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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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2020-10-15 10:13:54 +00:00
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- enable_conda:
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2020-08-07 14:05:25 +00:00
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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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2020-12-14 00:34:24 +00:00
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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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2019-12-05 14:18:09 +00:00
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input:
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2020-08-07 14:05:25 +00:00
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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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2019-12-05 14:18:09 +00:00
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output:
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2020-08-07 14:05:25 +00:00
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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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- 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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2019-12-05 14:18:09 +00:00
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authors:
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2020-08-07 14:05:25 +00:00
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- "@drpatelh"
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- "@grst"
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- "@ewels"
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- "@FelixKrueger"
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