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Start work on FastQC module files
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4 changed files with 34 additions and 17 deletions
2
.github/workflows/test-processes.yml
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2
.github/workflows/test-processes.yml
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@ -15,4 +15,4 @@ jobs:
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- name: FastQC
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path: tools/fastqc/*
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uses: ./tools/fastqc/test-action.yml
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run: nextflow run ./tools/fastqc/test/
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@ -1,19 +1,3 @@
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/*
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* Description:
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* Run FastQC on sequenced reads
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* Keywords:
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* read qc
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* adapter
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* Tools:
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* FastQC:
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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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* description: 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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*/
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process fastqc {
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tag "$sample_id"
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publishDir "${params.outdir}/fastqc", mode: 'copy',
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32
tools/fastqc/meta.yml
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32
tools/fastqc/meta.yml
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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: hhttps://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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input:
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-
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- sample_id:
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type: string
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description: Sample identifier
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- reads:
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type: file
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description: Input FastQ file, or pair of files
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output:
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-
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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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- @ewels
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1
tools/fastqc/test/main.nf
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1
tools/fastqc/test/main.nf
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/* A mini pipeline to test FastQC here */
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