Up: Component summary
Up: Component summary
Component
FastQCShort reads quality control for high-throughput sequencing data. Performs FastQC quality control analysis for DNA-seq or RNA-seq reads from whole genome (WGS) or targeted (exome) sequencing. It supports running FastQC in either interactive or non-interactive mode. In interactive mode, FastQC tool needs to be installed.
Set number of threads with annotation ._custom("cpu")="[no_of_threads]". Example: instance._custom("cpu")="4"
| Version | 2.0 |
|---|---|
| Bundle | sequencing |
| Categories | Quality control |
| Authors | Ping Chen (ping.chen@helsinki.fi), Alejandra Cervera (alejandra.cervera@helsinki.fi) |
| Issue tracker | View/Report issues |
| Requires | jbzip2-0.9.jar (jar) ; sam-1.32.jar (jar) ; rnaSeq.jar (jar) ; installer (bash) |
| Source files | component.xml FastQC.java |
| Usage | Example with default values |
Inputs| Name | Type | Mandatory | Description |
|---|---|---|---|
| read | FASTQ | Mandatory | FASTQ file containing unpaired reads or the #1 mates for paired-end input. |
| mate | FASTQ | Optional | FASTQ file containing the #2 mates for paired-end input. |
Outputs| Name | Type | Description |
|---|---|---|
| summary | Array<TextFile> | An array with summary files on the qualities of each input sequence file. The key should be 'read' and 'mate' for pair-end reads and only 'read' for single end. |
| report | Latex | A latex report on the sequence quality. |
| extra | CSV | A CSV file records with extra information. |
| folder | BinaryFolder | Original output folder from FastQC, if clean parameter is set to true this folder will be empty. |
Parameters| Name | Type | Default | Description |
|---|---|---|---|
| clean | boolean | true | A boolean for cleaning all meta data. If you want to have the html report or input the output folder to QCFasta then set it to false. |
| interactive | boolean | false | A boolean demonstrates if it will be run in an interactive way. The default is: false. No graphic interface will be displayed. |
| pagebreak | boolean | true | Determines if the result document should end with a page break. |
| sectionType | string | "subsection" | Type of LaTeX section: usually one of section, subsection or subsubsection. No section statement is written if sectionTitle is empty. |
| suffix | string | "" | A string to be added to the figure folders in latex report. |
Test cases| Test case | Parameters▼ | IN read |
IN mate |
OUT summary |
OUT report |
OUT extra |
OUT folder |
|---|---|---|---|---|---|---|---|
| case1 | properties | read | mate | summary | (missing) | extra | (missing) |
|
suffix=case1, |
|||||||
| case2 | (missing) | read | (missing) | summary | (missing) | extra | (missing) |
| case3 | properties | read | (missing) | summary | (missing) | extra | (missing) |
|
clean=false |
|||||||
| case4 | properties | read | mate | summary | (missing) | extra | (missing) |
|
suffix=case1, |
|||||||
| case_fail | (missing) | read | (missing) | (expecting failure) | (expecting failure) | (expecting failure) | (expecting failure) |