snakefile.smk

import enum
from typing import List
from pathlib import Path


class Alignment(enum.Enum):
   BWA = 1
   Bowtie = 2
    
class VariantCalling(enum.Enum):
   HaplotypeCaller = 1
   Manta = 2
  
class Annotation(enum.Enum):
   SnpEff = 1
   Coovar = 2
  
terminal_files: List[Path] = []

 
# Implementation #1: parse the config object to get the list of tools and run all combinations
# (ex. "bwa,bowtie,hc,manta")
alignment_tools: List[Alignment] = [Alignment(name) for name in config["alignment"].split(",")]
variant_calling_tools: List[Alignment] = [VariantCalling(name) for name in config["variant_calling"].split(",")]
annotation_tools: List[Alignment] = ...
annotation_tools: List[Alignment] = ...
for alignment_tool in alignment_tools:
  for variant_calling_tool in variant_calling_tools:
    for annotation_tool in annotation_tools:
      terminal_files.append(f"sample.{alignment_tool}.{variant_calling_tool}.{annotation_tool}.vcf.gz")
      
# Implementation #2: user specifies the combination list to use (ex. "bwa:hc:coovar,bwa:manta:snpeff")
for tool_chain in config["tool_chains"].split(",")
  alignment_tool, variant_calling_tool, annotation_tool = tool_chain.split(":")
  terminal_files.append(f"sample.{alignment_tool}.{variant_calling_tool}.{annotation_tool}.vcf.gz")

# rules

rule all:
  input:
    terminal_files
  

rule bwa:
  input:
    r1 = "{sample}.fastq.gz",
    r2 = "{sample}.fastq.gz"
  output:
    bam = "{sample}.bwa.bam"
    
rule bowtie:
  ...

rule hc:
  input:
    bam = "{sample}.bam"
  output:
    vcf = "{sample}.hc.vcf.gz"
    ...
    
rule manta:
   input:
    vcf = "{sample}.vcf"
  output:
    vcf = "{sample}.manta.vcf.gz"
    ...

rule coovar:
  ...
  
# rules for annotation similarly, exercise left to the reader