crosscheckFingerprintCaller

To call sequencing library swaps and matches from CrosscheckFingerprints output given OICR metadata.

Overview

Dependencies

• crosscheck_fingerprint_caller
• jq

Usage

Cromwell

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

Inputs

Required workflow parameters:

Parameter	Value	Description
crosscheckFingerprints	Array[File]	CrosscheckFingerprints input files
metadata	Array[Map[String,String]]	Metadata to add to the CrosscheckFingerprints data
ambiguous	Array[Map[String,String]]	The ambiguous LOD ranges for each library design pair
outputFileNamePrefix	String	String to add to the output file names

Optional workflow parameters:

Parameter	Value	Default	Description
seperator	String	";"	Which character is used to seperate multiple batches

Optional task parameters:

Parameter	Value	Default	Description
writeAmbiguousRange.timeout	Int	1	The hours until the task is killed.
writeAmbiguousRange.memory	Int	1	The GB of memory provided to the task.
writeAmbiguousRange.threads	Int	1	The number of threads the task has access to.
writeAmbiguousRange.modules	String	"jq/1.6"	The modules that will be loaded.
writeMetadata.timeout	Int	1	The hours until the task is killed.
writeMetadata.memory	Int	1	The GB of memory provided to the task.
writeMetadata.threads	Int	1	The number of threads the task has access to.
writeMetadata.modules	String	"jq/1.6"	The modules that will be loaded.
runMain.timeout	Int	1	The hours until the task is killed.
runMain.memory	Int	1	The GB of memory provided to the task.
runMain.threads	Int	1	The number of threads the task has access to.
runMain.modules	String	"crosscheck-fingerprint-caller/0.2.0"	The modules that will be loaded.

Outputs

Output	Type	Description	Labels
calls	File	CSV file with metadata and swap calls for each library	vidarr_label: calls
detailed	File	CSV file with metadata and detailed swap calls for each library pair	vidarr_label: detailed

Commands

See WDL

Support

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

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