removing multiple inclusion of common.smk

workflow/Snakefile

@@ -13,6 +13,8 @@ samples = glob_wildcards(config["hic_path"] + samples_in_pattern).sample
 # set {diploid_mode} global variable - used to run hifiasm_het rather than hifiasm
 diploid_mode=config["hifiasm"]["optional_params"]["--h1"] and config["hifiasm"]["optional_params"]["--h2"]
 
+# Include the common rule, where the inputs for rule_all are defined
+include: "rules/common.smk"
 # Include the hifi_prep rule
 include: "rules/hifi_prep.smk"
 # Include the nanoplot
@@ -45,8 +47,6 @@ include: "rules/two_read_bam_combiner.smk"
 include: "rules/picard.smk"
 # Include the yahs rule
 include: "rules/yahs.smk"
-# Include the common rule, where the inputs for rule_all are defined
-include: "rules/common.smk"
 
 
 # Define the rule all, which is the default rule that Snakemake runs when no specific rule or target is specified

workflow/rules/bwa_index.smk

@@ -4,9 +4,6 @@
 # colora doesn't contain the codes to handle technical and biological replicates of hic reads, refer to the original pipeline for that
 
 
-# include common.smk to use wildcards
-include: "common.smk"
-
 rule bwa_index:
     input:
         get_bwa_index_inputs

workflow/rules/common.smk

@@ -41,7 +41,7 @@ def get_all_inputs(wc=None):
         ))  # final scaffolded assembly
 
     # If not in diploid mode, add asm.alternate.fa as an input
-    if not diploid_mode:
+    if not diploid_mode and config["include_purge_dups"] == True:
         inputs.append("results/purge_dups_alt/asm.alternate_purged.fa")
 
     return inputs

workflow/rules/oatk.smk

@@ -1,9 +1,5 @@
 # This rule runs oatk to extract organelles reads from the hifi reads.
 
-# include common.smk to use get_oatk_outputs function
-# get_oatk_outputs is used to dynamically decide the outputs of oatk
-include: "common.smk"
-
 
 rule oatk:
     input:

workflow/rules/purge_dups.smk

@@ -1,10 +1,5 @@
 # This rule uses purge_dups purge haplotigs and overlaps from the primary assembly produced by hifiasm
 
-
-# include common.smk to use get_purge_dups_inputs
-include: "common.smk"
-
-
 rule purge_dups:
     input:
         reads="results/reads/hifi/hifi.fastq.gz",

workflow/rules/yahs.smk

@@ -2,11 +2,6 @@
 
 import glob
 
-
-# include common.smk to use get_bwa_index_inputs
-include: "common.smk"
-
-
 rule yahs:
     input:
         REF="results/bwa_index_{hap}/asm.fa",