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longranger

Currently supported Longranger pipelines:

  • wgs
  • targeted
  • align

Usage:

longranger wgs --fastqs=/path/to/fastq --id=NA12878
multiqc /path/to/NA12878

This module will look for the files _invocation and summary.csv in the the NA12878 folder, i.e. the output folder of Longranger in this example. The file summary.csv is required. If the file _invocation is not found the sample will receive a generic name in the MultiQC report (longranger#1), instead of NA12878 or whatever was given by the --id parameter.