R/purple_full.R

In msubirana/ergWgsTools: What the Package Does (One Line, Title Case)

purple_full <- function(control_name,
                        control,
                        tumor_name,
                        tumor,
                        output_dir_cobalt,
                        threads,
                        output_dir_amber,
                        output_dir_gridss,
                        refgen,
                        strelka_snvs,
                        strelka_indels,
                        strelka_merged,
                        strelka_merged_annotated,
                        strelka_merged_annotated_reheader,
                        strelka_merged_annotated_reheader_pass,
                        output_dir_purple){

  # cobalt(control_name=control_name,
  #        control=control,
  #        tumor_name=tumor_name,
  #        tumor=tumor,
  #        output_dir_cobalt=output_dir_cobalt,
  #        threads=threads)
  #
  # amber(control_name=control_name,
  #       control=control,
  #       tumor_name=tumor_name,
  #       tumor=tumor,
  #       output_dir_amber=output_dir_amber,
  #       threads=threads)
  #
  #
  # mergeStrelka(refgen=refgen,
  #              strelka_snvs=strelka_snvs,
  #              strelka_indels=strelka_indels,
  #              control_name=control_name,
  #              strelka_merged=strelka_merged,
  #              strelka_merged_annotated=strelka_merged_annotated,
  #              strelka_merged_annotated_reheader_pass=strelka_merged_annotated_reheader_pass,
  #              tumor_name=tumor_name,
  #              strelka_merged_annotated_reheader=strelka_merged_annotated_reheader)

  gridss(control_name=control_name,
         control=control,
         tumor_name=tumor_name,
         tumor=tumor,
         output_dir_gridss=output_dir_gridss,
         threads=threads)

  # purple(control_name=control_name,
  #        control=control,
  #        tumor_name=tumor_name,
  #        tumor=tumor,
  #        output_dir_purple=output_dir_purple,
  #        output_dir_cobalt=output_dir_cobalt,
  #        output_dir_amber=output_dir_amber,
  #        threads=threads,
  #        somatic_vcf=strelka_merged_annotated_reheader)

}