fastQC

Niassa-wrapped Cromwell (widdle) workflow for running FastQC tools on paired or unpaired reads.

Dependencies

• fastqc 0.11.9

Usage

Cromwell

java -jar cromwell.jar run fastqc.wdl --inputs inputs.json

Inputs

Required workflow parameters:

Parameter	Value	Description
fastqR1	File	Input file with the first mate reads.

Optional workflow parameters:

Parameter	Value	Default	Description
fastqR2	File?	None	Input file with the second mate reads (if not set the experiments will be regarded as single-end).
outputFileNamePrefix	String	""	Output prefix, customizable. Default is the first file's basename.
r1Suffix	String	"_R1"	Suffix for R1 file.
r2Suffix	String	"_R2"	Suffix for R2 file.

Optional task parameters:

Parameter	Value	Default	Description
firstMateFastQC.jobMemory	Int	6	Memory allocated to fastqc.
firstMateFastQC.timeout	Int	20	Timeout in hours, needed to override imposed limits.
firstMateFastQC.javaHeap	Int	4	Memory allocated to java heap, in G.
firstMateFastQC.threads	Int?	None	Threads param for fastqc
firstMateFastQC.modules	String	"perl/5.28 java/11 fastqc/0.11.9"	Names and versions of required modules.
firstMateHtml.jobMemory	Int	2	Memory allocated to this task.
firstMateHtml.timeout	Int	1	Timeout, in hours, needed to override imposed limits.
firstMateZip.jobMemory	Int	2	Memory allocated to this task.
firstMateZip.timeout	Int	1	Timeout, in hours, needed to override imposed limits.
secondMateFastQC.jobMemory	Int	6	Memory allocated to fastqc.
secondMateFastQC.timeout	Int	20	Timeout in hours, needed to override imposed limits.
secondMateFastQC.javaHeap	Int	4	Memory allocated to java heap, in G.
secondMateFastQC.threads	Int?	None	Threads param for fastqc
secondMateFastQC.modules	String	"perl/5.28 java/11 fastqc/0.11.9"	Names and versions of required modules.
secondMateHtml.jobMemory	Int	2	Memory allocated to this task.
secondMateHtml.timeout	Int	1	Timeout, in hours, needed to override imposed limits.
secondMateZip.jobMemory	Int	2	Memory allocated to this task.
secondMateZip.timeout	Int	1	Timeout, in hours, needed to override imposed limits.

Outputs

Output	Type	Description
html_report_R1	File	HTML report for the first mate fastq file.
zip_bundle_R1	File	zipped report from FastQC for the first mate reads.
html_report_R2	File?	HTML report for read second mate fastq file.
zip_bundle_R2	File?	zipped report from FastQC for the second mate reads.

Commands

This section lists command(s) run by fastqc workflow

• Running fastqc

fastqc workflow runs the following command (excerpt from .wdl file). INPUT_FASTQ is a placeholder for an input file.

FASTQC=$(which fastqc)
JAVA=$(which java)
perl $FASTQC INPUT_FASTQ --java=$JAVA --noextract --outdir "."

Support

For support, please file an issue on the Github project or send an email to [email protected] .

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