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fastQC

Cromwell (WDL) workflow for running FastQC tools on paired or unpaired reads. fastqc flowchart

Dependencies

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 Labels
html_report_R1 File HTML report for the first mate fastq file. vidarr_label: html_report_R1
zip_bundle_R1 File zipped report from FastQC for the first mate reads. vidarr_label: zip_bundle_R1
html_report_R2 File? HTML report for read second mate fastq file. vidarr_label: html_report_R2
zip_bundle_R2 File? zipped report from FastQC for the second mate reads. vidarr_label: zip_bundle_R2

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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