Check completed - nextflow comparison with main using hg38 (#25)

* revert some files to main.

* fix the known sorting issue.

* make process_gene same as main_fix_sort branch

* conf4 are now the same.

* force var_grp to be sorted by the index.

* fetching bin/generate_new_matrix_2.py from nextflow_coversion, checked output. (#26)

* Revert 27 hj/nxf comp/update bivar (#28)

* Hj/nxf comp/update bivar (#27)

* revert some files to main.

* fix the known sorting issue.

* make process_gene same as main_fix_sort branch

* conf4 are now the same.

* force var_grp to be sorted by the index.

* add indexing sorting for the var index.

* temporal off of the dedup.

* change the sorting for index of each group df.

* make confidence sorting stable.

* Revert "Hj/nxf comp/update bivar (#27)"

This reverts commit 95af064.

* pulling nextflow_conversion branch files.