small refactoring

config/config.yaml

@@ -70,7 +70,7 @@ genefusion:
 indel:
   activate: true # whether (=true) or not (=false) to include indels
   type: long # long, short, all
-  mode: BOTH  # DNA, RNA or BOTH - 
+  mode: RNA  # DNA, RNA or BOTH - 
   # strategy for optimizing posterior probability threshold
   strategy: OPTIMAL_F_SCORE # OPTIMAL_F_SCORE, FALSE_DISCOVERY_RATE, CONSTANT 
   fscorebeta: 1.0  # rel. weight of recall to precision (when OPTIMAL_F_SCORE is selected)

workflow/Snakefile

@@ -6,7 +6,12 @@ min_version("6.4.1")
 #### setup #######
 configfile: "config/config.yaml"
 
+rule all:
+  input:
+    expand("results/{sample}/neoantigens/results.tsv", sample=config['data']['name'])
+
 #### load rules ####
+include: "rules/all.smk"
 include: "rules/ref.smk"
 include: "rules/common.smk"
 include: "rules/hlatyping.smk"

workflow/rules/neoantigen.smk

@@ -26,16 +26,12 @@ rule variants_to_peptides:
   conda:
     "../envs/variants_to_peptides.yml"
   params:
-    length="-l {config['priorization']['mhc_i']['len']}"
+    length="{config['priorization']['mhc_i']['len']}"
   shell:
     """
-      python3 workflow/scripts/variants_to_peptide.py \
-          -v {input.var} -o {output} \
+      python3 workflow/scripts/variants_to_peptides.py \
+          -v '{input.var}' -o {output} \
           -a {input.alleles} \
           -o {output} \
-          {params.length} > {log}
+          -p 8-11 > {log}
     """
-
-rule all:
-  input:
-    "results/{sample}/neoantigens/results.tsv"