Incorrect Fonda behavior in asynchronous mode

[kamyshova]

Background

When Fonda is launching in asynchronous mode some of the tasks executed in asynchronous mode accordingly.
For example, a piece of code from DnaCaptureVar_Fastq_postalignment_for_SampleTest1_analysis.sh script:

qsub DnaCaptureVar_Fastq_vardict_for_SampleTest1_analysis.sh 

if [ $? -eq 0 ] 
then 
echo `date` Successful Step: Run vardict. 
sleep 8 
else 
echo `date` Error Step: Run vardict. 
echo `date` The job was aborted due to ERRORS found. 
exit 1; 
fi 
 
echo `date` Begin Step: Remove temporary directories... 
rm -rf DnaCaptureVar_Fastq_test/SampleTest1/bam/SampleTest1.merged.sorted.bam 

The problem is that SampleTest1.merged.sorted.bam is used in DnaCaptureVar_Fastq_vardict_for_SampleTest1_analysis.sh. And by the time the Vardict starts using this bam, bam will already be deleted in the script.

Approach

In this case, we assume that the simplest way is to change the success check of the tool run. Add a "Successful Step/Error Step" wait for tool log file check.