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

Fetched 2021-05-30 13:47:04 GMT

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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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 Label 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

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