minimap2

Workflow to align the fastq file to a reference genome

Overview

Dependencies

Usage

Cromwell

java -jar cromwell.jar run minimap2.wdl --inputs inputs.json

Inputs

Required workflow parameters:

Parameter	Value	Description
`ref`	String	the reference file name used for alignment
`fastqFile`	File	a fastq file to be aligned

Optional workflow parameters:

Parameter	Value	Default	Description
`outputFileNamePrefix`	String	basename(basename(fastqFile,".gz"),".fastq")	Variable used to set the name of the outputfile
`additionalParameters`	String?	None	Additional parameters to be added to the minimap2 command

Optional task parameters:

Parameter	Value	Default	Description
`align.minimap2`	String	"minimap2"	minimap2 module name to use.
`align.modules`	String	"minimap2/2.17"	Environment module names and version to load (space separated) before command execution.
`align.memory`	Int	31	Memory (in GB) allocated for job.
`align.timeout`	Int	24	Runtime for the job in hours.
`sam2Bam.samtools`	String	"samtools"	samtools module name to use.
`sam2Bam.modules`	String	"samtools/1.9"
`sam2Bam.memory`	Int	31	Memory (in GB) allocated for job.
`sam2Bam.timeout`	Int	24	Runtime for the job in hours.

Outputs

Output	Type	Description
`bam`	File	output of samtools in .bam format
`bamIndex`	File	index of the bam file

Niassa + Cromwell

This WDL workflow is wrapped in a Niassa workflow (https://github.com/oicr-gsi/pipedev/tree/master/pipedev-niassa-cromwell-workflow) so that it can used with the Niassa metadata tracking system (https://github.com/oicr-gsi/niassa).

Building

mvn clean install

Testing

mvn clean verify -Djava_opts="-Xmx1g -XX:+UseG1GC -XX:+UseStringDeduplication" -DrunTestThreads=2 -DskipITs=false -DskipRunITs=false -DworkingDirectory=/path/to/tmp/ -DschedulingHost=niassa_oozie_host -DwebserviceUrl=http://niassa-url:8080 -DwebserviceUser=niassa_user -DwebservicePassword=niassa_user_password -Dcromwell-host=http://cromwell-url:8000

Support

For support, please file an issue on the Github project or send an email to gsi@oicr.on.ca .

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