Create SeqMonk Projects

[ewels]

It would be great if we could add a step at the end of the pipeline to automatically create a SeqMonk project.

Not sure if this will be possible due to requiring a SeqMonk installation with reference genomes. Could make it optional? Or just ignore a failure?

SeqMonk importer docs:

      SeqMonk Importer - Creating SeqMonk Projects from the command line
SYNOPSIS
	seqmonk [--(un)spliced] [--mapq=20] --genome "Mus musculus/GRCm38" --outfile out.smk *.bam
DESCRIPTION
	This script allows you to run seqmonk in a non-interactive mode to read in
	a number of BAM or Bismark coverage files and save these into a single project 
	file which you can then transfer to an interactive server to do further 
	downstream analysis.
    
    The options for the program as as follows:
    --genome        The genome to use for the import.  This is specified as
                    species/assembly and must match an existing genome in your
                    seqmonk genomes folder.
	               
    --outfile       The name of the file you want to write the project to
    --spliced       Split spliced reads so you only see the exonic parts. Will
                    be added by default if any of the first 100,000 reads in
                    the first imported BAM file have a splice site in them. 
                    Adding this flag overrides the auto-detection.
	                
    --unspliced     No not split spliced reads even if they are present.  This
                    flag overrides the default auto-detection.
	                
    --mapq          Value to use as a MAPQ cutoff for imported reads.  Defaults
                    to 20 if any of the first 100,000 reads has a value above 20.
    -h --help       Print this help file and exit
    
    -m --memory     Set the starting memory allocation in megabytes. Defaults
                    to 1300. Minimum allowed value is 500 and values above
                    1300 should only be set on systems running a 64-bit JRE