Remove unnecessary intermediate outputs

[mfoll]

The only important outputs are: the final VCF and PDF files. All other intermediate files should only be present in nextflow work directory. This will imply:

• removing storeDir directives in split_bed, samtools_mpileup and mpileup2table processes
• deleting the intermediate VCF outputs at the end of collect_vcf_result (see how we delete the empty pdf files).
• renaming the VCF output dir as PDF
• deleting the PDF folder and the all_variants.vcf file as the first step in the pipeline

It will has the advantage that the pipeline will be restarted from the beginning by default. We should note in the manual that the output is erased when it exists already. Users will still have the option to resume an interrupted pipeline by adding the -resume option to the command line (add that to the manual too).

[mfoll]

See nextflow-io/nextflow#81

[mfoll]

Now that we use publishDir, my 4th point above is no longer necessary as the default behaviour is (https://github.com/nextflow-io/nextflow/blob/master/docs/process.rst#publishdir):

any existing file in the specified folder will be overridden (default: true during normal pipeline execution and false when pipeline execution is resumed).

[tdelhomme]

Yes it's true.
Also I modified the script as you mentionned.