fix: use homopolymer-pair-HMM-mode of Varlociraptor in case of nanopo…

…re reads (#587)

* Revert "Revert "fix: use homopolymer-pair-HMM-mode of Varlociraptor in case of nanopore reads""

This reverts commit 91274a5.

* properly retrieve sample data frame

* use pep sample table

* fix typo

* fix technology call

---------

Co-authored-by: Alex Thomas <[email protected]>

workflow/rules/common.smk

@@ -1592,6 +1592,16 @@ def get_checked_mode():
     raise TypeError(f'Mode {mode} not recognized. Can be "patient" or "environment".')
 
 
+def get_varlociraptor_preprocess_flags(wildcards):
+    technology = get_technology(wildcards)
+    if technology == "ont":
+        return "--pairhmm-mode homopolymer"
+    elif technology == "illumina" or technology == "ion":
+        return ""
+    else:
+        raise NotImplementedError(f"Technology {technology} not supported.")
+
+
 def get_input_by_mode(wildcard):
     paths = [
         expand(

workflow/rules/variant_calling.smk

@@ -143,12 +143,13 @@ rule varlociraptor_preprocess:
         temp("results/{date}/observations/ref~{reference}/{sample}.{varrange}.bcf"),
     params:
         depth=config["variant-calling"]["max-read-depth"],
+        extra=get_varlociraptor_preprocess_flags,
     log:
         "logs/{date}/varlociraptor/preprocess/ref~{reference}/{sample}.{varrange}.log",
     conda:
         "../envs/varlociraptor.yaml"
     shell:
-        "varlociraptor preprocess variants --candidates {input.candidates} "
+        "varlociraptor preprocess variants {params.extra} --candidates {input.candidates} "
         "{input.ref} --bam {input.bam} --max-depth {params.depth} --output {output} 2> {log}"