Up: Component summary Component

FastQC

Short reads quality control. It supports to run FastQC in either interactive or non-interactive mode. In interactive mode, FastQC tool needs to be installed.

Set number of treads 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,
clean=false

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,
clean=false

case_fail (missing) read (missing) (expecting failure) (expecting failure) (expecting failure) (expecting failure)

Generated 2018-12-11 07:42:06 by Anduril 2.0.0