add data type input, update for function changes

[Chunmingl]

• updated a few steps for function changes from adjust_susie_weights and allele_qc.
  • adjust_susie_weights had input updated with input object specified by pipeline-specific input
  • allele_qc function requires the target data to have the variant information columns (chrom, pos, A1, A2), while our target for harmonizations can be weight matrices that do not have these columns. Some steps are added for checking and adding these required columns.
• add --xqtl_type_table for xqtl type mapping, with two column (file, type) table, then we will have the data type information for ctwas weights list generation.

below is an example for after adding data type to the output1 of the pipeline - refined_twas_weights_data

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