ngs_pipeline.opt

reference: /vlsci/VLSCI/bjpop/scratch/references/kat.holt/Klebs_MGH78578_withPlasmid.mfasta
sequences: /vlsci/VLSCI/bjpop/scratch/sequences/kat.holt/*.fastq
pipeline:
   logDir: log
   logFile: pipeline.log
   style: run
   procs: 8
   paired: True
stageDefaults:
   distributed: False
   walltime: "02:00:00"
   memInGB: 10
   modules:
      - "bwa-gcc"
      - "samtools-gcc/0.1.8"
stages:
   mkRefDataBase:
      command: "lambda ref, out: 'bwa index %s -a bwtsw' % ref"
   alignSequence:
      command: "lambda ref, seq, out: 'bwa aln -t 8 %s %s > %s' % (ref, seq, out)"
      walltime: "06:00:00"
      queue: smp
   alignToSam:
      command: "lambda ref, align1, align2, seq1, seq2, out: 'bwa sampe %s %s %s %s %s > %s' % (ref, align1, align2, seq1, seq2, out)"
   samToBam:
      command: "lambda ref, sam, out: 'samtools import %s %s %s' % (ref, sam, out)"
   sortBam:
      command: "lambda bam, out: 'samtools sort %s %s' % (bam, out)"
   pileupFull:
      command: "lambda ref, bam, out: 'samtools pileup -cf %s %s > %s' % (ref, bam, out)"
   callSNPs:
      command: "lambda ref, bam, out: 'samtools pileup -vcf %s %s > %s' % (ref, bam, out)"
   varFilter:
      command: "lambda fullPileup, varPileup, chromName, chromLength, out: './varFilter %s %s %s %s %s' % (fullPileup, varPileup, chromName, chromLength, out)"