#error: perform_de is not taking ensembl mapping file

[nfancy]

perform_de function is not taking the mappings_filepath arguments from map_ensembl_gene_id. Need to fix asap as biomaRt is down and perform_de is failing each time.

[nfancy]

Made a minor change in the perform_de script.

changed the function from

ensembl_res <- map_ensembl_gene_id(
      fcHurdle$ensembl_gene_id,
      mappings = c("external_gene_name", "gene_biotype")) %>%
      dplyr::rename(gene = external_gene_name)

to this

ensembl_res <- map_ensembl_gene_id(
      fcHurdle$ensembl_gene_id,
      mappings = c("external_gene_name", "gene_biotype"),
      ensembl_mapping_file = fargs$ensembl_mapping_file
    ) %>%
      dplyr::rename(gene = external_gene_name)

Also a minor change in the map_ensembl_gene_id function. Changed mappings_file argument to ensembl_mapping_file to make it across other function arguments.

commit # 291bae1