Workflow: FastQC - a quality control tool for high throughput sequence data
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
- Selected
- |
- Default Values
- Nested Workflows
- Tools
- Inputs/Outputs
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 |
https://w3id.org/cwl/view/git/e0a30aa1ad516dd2ec0e9ce006428964b840daf4/workflows/fastqc.cwl