parser.add_argument("-output",help="Target directory for the pipeline results",required=True)
parser.add_argument("-reference",help="Reference for alignment and statistics")
parser.add_argument("-size",help="The size for cutting region (default: 2000)",default='2000')
parser.add_argument("-list",help="A list of regions to work on (format: [r1, r2, ...] or [rStart_End, ...]) (default: no region)")
parser.add_argument("-size",help="The desired region size (default: 2000)",default='2000')
parser.add_argument("-tools",help="The list of tools to use in the meta-consensus (default: ['abpoa', 'spoa', 'kalign2', 'kalign3', 'mafft', 'muscle'])",default="['abpoa', 'spoa', 'kalign2', 'kalign3', 'mafft', 'muscle']")
parser.add_argument("-consensus_threshold",help="Threshold(s) used for the MSA consensus step (default: [70])",default="[70]")
parser.add_argument("-metaconsensus_threshold",help="Threshold(s) used for the Meta-consensus result (default: [60])",default="[60]")
parser.add_argument("-depth",help="The depth used in the process (default: [60])",default="[60]")
parser.add_argument("-plot",help="Analyse the meta-consensus and MSA consensus quality (requires reference)")
parser.add_argument("-plot",help="Analyse the meta-consensus and MSA consensus quality (requires reference)",action='store_true')
parser.add_argument("-region_overlap",help="The size of the overlap between regions",default="50")
parser.add_argument("-cores",help="The amount of cores to use in the pipeline run (default 1)",default=1)
message: "Exonerate comparison between meta-consensus and ref (region: {wildcards.region}, or preliminary consensus threshold in [ {config[threshold_1]} ], meta-consensus threshold in [ {config[threshold_2]} ]"
message: "Exonerate comparison between meta-consensus and ref (region: {wildcards.region}, or preliminary consensus threshold in [ {config[threshold_1]} ], meta-consensus threshold in [ {config[threshold_2]} ]"
message: "Creating plot for meta-consensus quality with preliminary threshold in [ {config[threshold_1]} ] and meta-consensus in [ {config[threshold_2]} ] (region: {wildcards.region}, depth: {wildcards.depth})"
message: "Creating plot for meta-consensus compared to preliminary consensus with meta-consensus threshold in {config[threshold_2]} (region: {wildcards.region}, depth: {wildcards.depth}, threshold: {wildcards.threshold})"