adjusting with common

workflow/rules/bwa_index.smk

@@ -3,29 +3,8 @@
 # For more info: https://github.com/ArimaGenomics/mapping_pipeline
 # colora doesn't contain the codes to handle technical and biological replicates of hic reads, refer to the original pipeline for that
 
-
-# create a function to read the inputs of bwa_index rule dynamically 
-def get_bwa_index_inputs():
-    if config["include_purge_dups"] == 'True':
-        return "results/purge_dups/hifiasm_p_purged.fa"
-    else:
-        return "results/hifiasm/hifiasm.asm.p_ctg.fa"
-
-
-# create a function to read the outputs of bwa_index rule dynamically 
-def get_bwa_index_outputs():
-    if config["include_purge_dups"] == 'True':
-        return ["results/purge_dups/hifiasm_p_purged.fa.amb",
-                "results/purge_dups/hifiasm_p_purged.fa.ann",
-                "results/purge_dups/hifiasm_p_purged.fa.bwt",
-                "results/purge_dups/hifiasm_p_purged.fa.pac",
-                "results/purge_dups/hifiasm_p_purged.fa.sa"]
-    else:
-        return ["results/hifiasm/hifiasm.asm.p_ctg.fa.amb",
-                "results/hifiasm/hifiasm.asm.p_ctg.fa.ann",
-                "results/hifiasm/hifiasm.asm.p_ctg.fa.bwt",
-                "results/hifiasm/hifiasm.asm.p_ctg.fa.pac",
-                "results/hifiasm/hifiasm.asm.p_ctg.fa.sa"]
+# include common.smk to use get_bwa_index_inputs and get_bwa_index_outputs functions
+include: "common.smk"
 
 rule bwa_index:
     input: