catch errors when rnaseq is not provided (exitron/altsplicing calling…

…) and add reference genome index as input for indel calling (htcaller)

workflow/rules/common.smk

@@ -124,6 +124,7 @@ def all_identical(l):
 
 # load up the config
 config['data'] = data_structure(config['data'])
+print(config)
 
 ########### PREPROCESSING ##########
 def get_raw_reads(wildcards):
@@ -734,18 +735,22 @@ def get_prioritization_long_indels(wildcards):
 def get_prioritization_exitrons(wildcards):
   exitrons = []
   if config["exitronsplicing"]["activate"]:
-    exitrons += expand("results/{sample}/annotation/exitrons.vcf",
-                       sample=config["data"]["name"])
-
+    if len(config["data"]["rnaseq"]) != 0:
+      exitrons += expand("results/{sample}/annotation/exitrons.vcf",
+                         sample=config["data"]["name"])
+    else:
+      print('rnaseq data has not been specified in the config file, but exitron calling is activated - skipping...')
   return exitrons
 
 
 def get_prioritization_altsplicing(wildcards):
   altsplicing = []
   if config["altsplicing"]["activate"]:
-    altsplicing += expand("results/{sample}/annotation/altsplicing.vcf",
-                          sample=config["data"]["name"])
-
+    if len(config["data"]["rnaseq"]) != 0:
+      altsplicing += expand("results/{sample}/annotation/altsplicing.vcf",
+                            sample=config["data"]["name"])
+    else:
+      print('rnaseq data has not been specified in the config file, but alternative splicing calling is activated - skipping...')
   return altsplicing
 
 def get_prioritization_custom(wildcards):

workflow/rules/germline.smk

@@ -73,7 +73,8 @@ rule detect_variants_htc_first_round:
   input:
     bam="results/{sample}/{seqtype}/align/{group}_final_BWA_split/{chr}.bam",
     idx="results/{sample}/{seqtype}/align/{group}_final_BWA_split/{chr}.bam.bai",
-    ref="resources/refs/genome.fasta"
+    ref="resources/refs/genome.fasta",
+    ref_idx="resources/refs/genome.fasta.fai"
   output:
     vcf="results/{sample}/{seqtype}/indel/htcaller/{group}_variants.1rd/{chr}.vcf"
   message: