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
                        

$ nextflow run $NF/bismark.nf -profile base --reads '*_R{1,2}_001.fastq' --genome mm10 --rrbs

N E X T F L O W  ~  version 0.25.4
Launching `NGI-MethylSeq/bismark.nf` [crazy_monod] - revision: 566634b95a
==================================================
 NGI-MethylSeq : Bisulfite-Seq Best Practice v0.2
==================================================
...
[warm up] executor > local
ERROR ~ No such variable: bismark_dedup_log_1

 -- Check script 'bismark.nf' at line: 413 or see '.nextflow.log' file for more details

// Function to ensure that resource requirements don't go beyond
// a maximum limit
def check_max(obj, type) {
  if(type == 'memory'){
    if(obj.compareTo(params.max_memory) == 1)
      return params.max_memory
    else
      return obj
  } else if(type == 'time'){
    if(obj.compareTo(params.max_time) == 1)
      return params.max_time
    else
      return obj
  } else if(type == 'cpus'){
    return Math.min( obj, params.max_cpus )
  }
}