Single-end pipelines non-conditional

Adds new pipeline scripts, described in README.md

The new scripts include some features that could be more widely useful and adapted in other pipelines:

• runs pipeline_printout_graph for a graphical description of pipeline to flowchart.jpg
• runs fastqc on demultiplexed fastq files to count reads and assess quality
• runs bamqc on alignment files to assess alignment quality
• relies on novo putting out sam-format output with broad compatibility
• runs bamtools sort/index converting sam alignment files to bam files for input into genome browsers, bedtools, etc.
• runs multiBamCov from bedtools (uses pipeline merge, including keeping track of input file order in columns via the header)
• runs pyPileup.py if a genelist is supplied
• runs pyReadCounters.py twice, once with blocks and muts, once without.

These scripts avoid the conditional running allowed in original CRAC_pipeline_SE.py, because that was not playing well with pipeline_printout_graph.

CRAC_pipeline_SE_demultonly.py

CRAC pipeline for single-end reads, adapted by Edward Wallace, that does demultiplexing and not deduplicating. This adds extra QC and readout steps.

CRAC_pipeline_SE_demult_dedup.py

CRAC pipeline for single-end reads, adapted by Edward Wallace, that does both demultiplexing and deduplicating. This adds extra QC and readout steps.

test_pipeline_flexbar_SE.py

All this does is run flexbar on the input file, to test that you have ruffus and flexbar both work.