Change alfa output folder names

Changed alfa output folder names according to a dictionary introduced at the beginning of the snakefile with the aim of having more intuitive names later on in the multiqc report. Fixes #164 (closed)

workflow/Snakefile

@@ -1593,52 +1593,6 @@ rule alfa_qc:
         {params.additional_params}) \
         &> {log}"
 
-# current_rule = 'rename_alfa_folders'
-# rule rename_alfa_folders:
-#     input:
-#         tables = lambda wildcards:
-#             expand(
-#                 os.path.join(
-#                         config["output_dir"],
-#                         "samples",
-#                         "{sample}",
-#                         "ALFA",
-#                         alfa_dict["{renamed_unique}"]),
-#                     sample=wildcards.sample,
-#                     renamed_unique=alfa_dict.keys()
-#             ),
-#     output:
-#         tables = directory(
-#             os.path.join(
-#                 config["output_dir"],
-#                 "samples",
-#                 "{sample}",
-#                 "ALFA",
-#                 "{renamed_unique}",
-#                 )
-#             )
-#     params:
-#         cluster_log_path = config["cluster_log_dir"]
-
-#     log:
-#         stderr = os.path.join(
-#             config["log_dir"],
-#             "samples",
-#             "{sample}",
-#             current_rule + "_{renamed_unique}.stderr.log"),
-#         stdout = os.path.join(
-#             config["log_dir"],
-#             "samples",
-#             "{sample}",
-#             current_rule + "_{renamed_unique}.stdout.log")
-
-#     singularity:
-#         "docker://ubuntu:focal-20210416"
-
-#     shell:
-#         "(cp -r {input.tables} {output.tables};) \
-#          1>{log.stdout} 2>{log.stderr}"
-
 
 current_rule = 'prepare_multiqc_config'
 rule prepare_multiqc_config: