chain/dependency of some rules by wildcards - snakemake

Question

I have a particular use case for which I have not found the solution in the Snakemake documentation.
Let's say in a given pipeline I have a portion with 3 rules a, b and c which will run for N samples.
Those rules handle large amount of data and for reasons of local storage limits I do not want those rules to execute at the same time. For instance rule a produces the large amount of data then rule c compresses and export the results.
So what I am looking for is a way to chain those 3 rules for 1 sample/wildcard, and only then execute those 3 rules for the next sample. All of this to make sure the local space is available.
Thanks

Answer 1

I agree that this is problem that Snakemake still has no solution for. However you may have a workaround.
rule all:
input: expand("a{sample}", sample=[1, 2, 3])
rule a:
input: "b{sample}"
output: "a{sample}"
rule b:
input: "c{sample}"
output: "b{sample}"
rule c:
input:
lambda wildcards: f"a{wildcards.sample-1}"
output: "c{sample}"
That means that the rule c for sample 2 wouldn't start before the output for rule a for sample 1 is ready. You need to add a pseudo output a0 though or make the lambda more complicated.

Answer 2

So building on Dmitry Kuzminov's answer, the following can work (both with numbers as samples and strings).
The execution order will be a3 > b3 > a1 > b1 > a2 > b2.
I used a different sample order to show it can be made different from the sample list.
samples = [1, 2, 3]
sample_order = [3, 1, 2]
def get_previous(wildcards):
if wildcards.sample != sample_order[0]: # if different from a3 in this case
previous_sample = sample_order[sample_order.index(wildcards.sample) - 1]
return f'b_out_{previous_sample}'
else: # if is the first sample in the order i.e. a3
return #here put dummy file always present e.g. the file containing those rules or the Snakemake
rule all:
expand("b_out_{S}", S=sample)
rule a:
input:
"a_in_{sample}",
get_previous
output:
"a_out_{sample}"
rule b:
input:
"a_out_{sample}"
output:
"b_out_{sample}"