Problem:
In the shell script, the variable is called novoalign_options, however in the config json file, the variable is called aligner_options. Due to this inconsistency, the aligner option string is never passed to align_and_fix. This is confirmed via the logfile on DNAnexus, which reports the call, [...] -data/all.bam aligner_options= JVMmemory=4g [...] In the workflow setup, the variable is also called aligner_options.
Suggested resolution:
In the shell script, change novoalign_options to aligner_options.
Background: In the script for viral-ngs-assembly-analysis, an aligner option string is passed to
read_utils.py align_and_fixvia--aligner_options.Problem: In the shell script, the variable is called
novoalign_options, however in the config json file, the variable is calledaligner_options. Due to this inconsistency, the aligner option string is never passed toalign_and_fix. This is confirmed via the logfile on DNAnexus, which reports the call,[...] -data/all.bam aligner_options= JVMmemory=4g [...]In the workflow setup, the variable is also calledaligner_options.Suggested resolution: In the shell script, change
novoalign_optionstoaligner_options.