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Track qstat and directory to give progress of steps
Include key...to allow for shorter names for jobs.
The Rscript RMD has master which keeps track and regularly produces logs of states included errors and instant logs of fails and success.
Should capture output to console using capture.output as in my Rpres trainining/alignmentpart.RmD
Look for indexes longer than in run param..create new directory after trimming to minimum possible.
This happened in last run
Use Batchjobs or Biocparallel
That would take care of tracking but maybe not out.
Perhaps in config.
Would be advantatious to keep sub control in R rather then build stings in system2() calls
Move R into functions then a library we can version control.
Move RNA-seq or ChIP-seq Pipeline alignment and basic QC at end
Since we should know genome we can save a lot of time aligning and counting etc.
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