FastQC - a quality control tool for high throughput sequence data

Workflow: FastQC - a quality control tool for high throughput sequence data

Fetched 2023-01-10 20:15:57 GMT

Verified with cwltool version 3.1.20221201130942

FastQC - a quality control tool for high throughput sequence data ===================================== FastQC aims to provide a simple way to do some quality control checks on raw sequence data coming from high throughput sequencing pipelines. It provides a modular set of analyses which you can use to give a quick impression of whether your data has any problems of which you should be aware before doing any further analysis. The main functions of FastQC are: - Import of data from FastQ files (any variant) - Providing a quick overview to tell you in which areas there may be problems - Summary graphs and tables to quickly assess your data - Export of results to an HTML based permanent report - Offline operation to allow automated generation of reports without running the interactive application

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This workflow is Open Source and may be reused according to the terms of: Apache License 2.0

Note that the tools invoked by the workflow may have separate licenses.

Inputs

ID	Type	Title	Doc
alias	String	Experiment short name/Alias
fastq_file	File [FASTQ]	FASTQ file	Reads data in a FASTQ format, optionally compressed

Steps

ID	Runs	Doc
run_fastqc	../tools/fastqc.cwl (CommandLineTool)	Tool runs FastQC from Babraham Bioinformatics
extract_fastq	../tools/extract-fastq.cwl (CommandLineTool)	Tool to decompress input FASTQ file(s). If several FASTQ files are provided, they will be concatenated in the order that corresponds to files in input. Bash script's logic: - disable case sensitive glob check - check if root name of input file already include '.fastq' or '.fq' extension. If yes, set DEFAULT_EXT to \"\", otherwise use '.fastq' - check file type, decompress if needed - return 1, if file type is not recognized This script also works of input file doesn't have any extension at all
rename_fastqc_report	../tools/rename.cwl (CommandLineTool)	Tool renames `source_file` to `target_filename`. Input `target_filename` should be set as string. If it's a full path, only basename will be used. If BAI file is present, it will be renamed too

Outputs

ID	Type	Label	Doc
fastqc_report	File	FastqQC HTML report	FastqQC HTML report

Permalink: https://w3id.org/cwl/view/git/e0a30aa1ad516dd2ec0e9ce006428964b840daf4/workflows/fastqc.cwl