Class: SamtoolsIndexing

Inherits:

Object

• Object
• SamtoolsIndexing

Defined in:

lib/mutations_caller_pipeline_aws/samtools_indexing.rb

Class Method Summary

• .call(bam_file, job_prefix, account, debug, log_file) ⇒ Object

Class Method Details

.call(bam_file, job_prefix, account, debug, log_file) ⇒ Object

# File 'lib/mutations_caller_pipeline_aws/samtools_indexing.rb', line 2

def self.call(bam_file, job_prefix, account, debug, log_file)
  cmd = "qsub -o #{log_file} -V -cwd -b y -N indexing_#{job_prefix} -l h_vmem=3G -hold_jid bwa_#{job_prefix} #{account} \
    samtools index #{bam_file}"
  puts cmd
  system(cmd) if debug == 1
end