Create assoc-aggregate-one-gds.wdl

[akmanning]

Major changes from assoc-aggregate.wdl

workflow: assoc_agg_one_gds

• The expected gds and variant_group_file are for a single chromosome
• the Array[File] input_gds_files input was changed to File input_gds and likewise the Array[File] variant_group_files and variant_include_files was changed to File variant_group_file and variant_include_file
• the scatter across chromosomes was removed
• the sbg_prepare_segments_1 task is no longer necessary
• scattering across the segments is now simplified to scatter over an integer array (based on the number of actual segments for the chromosome
• added a default value for n_segments and n_segments must be between 1 and 10. The upper limit is arbitrary, but in order to make the segments feature work, n_segments is multiplied by 23 in the input to the define_segments.R
• required aggregate_type, chromosome, test inputs

Task assoc_aggregate

• simpler file inputs
• Int segment is now used
• the variant include file is calculated on the fly
• fixed the default out_prefix so that the output files have the form label.chrN.segN.RData (that format is expected in task assoc_combine_r