Hi, Not sure I'm asking this the right way but does anyone know a way to get a bash script to finish even if it fails? I'm trying to automate running a script on all the illumina R1 and R2 files in a directory, Using 1 script to batch together the pair of reads.
For R1 in *R1*.gz do Echo $R1 R2=`echo $R1 | sed 's/R1/R2/'` MyPipeline.sh "$R1" "$R2" Done
Mypipeline.sh then does denovo assembly, blasting a database to choose a reference, then mapping to that reference and creating a consensus sequence. My problem is that if the second script doesn't find a blast match it fails. The first script then doesn't move onto the next pair of raw reads. Please can anyone suggest a solution?