snakemake unpack with shell & conda - snakemake

Question

I have the basic "input can be single end or paired end reads" problem for my snakemake pipeline. I'd like to use unpack if possible, since it seems designed for this situation (as illustrated in the answer for this issue), but I also want to use conda:, which requires shell:. I believe that shell: will die if I have {input.read2} but it's not provided by unpack(). Is there any good way of getting around this besides either 1) creating 2 nearly identical rules 2) making an empty read2 (if single-end) and then creating an if-else in shell to check for whether read2 is empty. Neither is ideal.

Answer 1

Try to combine your input function with a params function to generate the flags for either paired or single end. Using the bowtie example from your link:
def bowtie2_inputs(wildcards):
if (seq_type == "pe"):
return expand("{reads}_{strand}.fastq", strand=["R1", "R2"], reads=wildcards.reads)
elif (seq_type == "se"):
return expand("{reads}.fastq", reads=wildcards.reads)
def bowtie2_params(wildcards, input):
if (seq_type == "pe"):
return f'-1 {input.reads[0]} -2 {input.reads[1]}'
else:
return f'-U {input.reads}'
rule bowtie2:
input:
reads=bowtie2_inputs,
index=bowtie2_index
output:
sam="{reads}_bowtie2.sam"
params:
file_args=bowtie2_params
conda: <env>
shell:
"bowtie2 -x {input.index} {params.file_args} -S {output.sam}"
Not sure it's any better than the shell option. I would use two rules with a ruleorder preferring the paired ends. That would be easier to modify if you wanted say a different aligner or to change parameters for each case. As is this requires a bit of jumping around to actually see what the rule does.