snakemake with prefix as output including a path - snakemake

Question

How can I make sure in rule all that the output folder was well created?
Should I add each expected result file?
somehow relates to snakemake define folder as output but in my case the specified 'output' is a combination of a path to a dir and a prefix for all results files (they wil be multiple)
the following command creates a folder path Analysis/MosDepth and adds to that path the files:
gt0.mosdepth.global.dist.txt
gt0.mosdepth.region.dist.txt
gt0.per-base.bed.gz
gt0.per-base.bed.gz.csi
gt0.regions.bed.gz
gt0.regions.bed.gz.csi
rule MosDepth:
input:
bam = "Analysis/Minimap2/"+UnpackedRawFastq+".bam",
bed = "ReferenceData/"+UnpackedGenomeGFF+"_exons.bed"
output:
pfx = "Analysis/MosDepth/gt0"
threads: config["threads"]
shell:
"mosdepth -t {threads} -b {input.bed} {output.pfx} {input.bam}"
I currently have only one of the files in rule all:, is this enough or is there a better way to ensure that the mosdepth has run well and not redo it in a later re-run?
rule all:
input:
"Analysis/MosDepth/gt0.regions.bed.gz"

Answer 1

I would recommend sth like this:
mos_out = ['gt0.mosdepth.global.dist.txt', 'gt0.mosdepth.region.dist.txt', 'gt0.per-base.bed.gz', 'gt0.per-base.bed.gz.csi', 'gt0.regions.bed.gz', 'gt0.regions.bed.gz.csi']
rule MosDepth:
input:
bam = "Analysis/Minimap2/"+UnpackedRawFastq+".bam",
bed = "ReferenceData/"+UnpackedGenomeGFF+"_exons.bed"
output:
expand("Analysis/MosDepth/{mos_out}", mos_out=mos_out)
params:
pfx = "Analysis/MosDepth/gt0"
threads: config["threads"]
shell:
"mosdepth -t {threads} -b {input.bed} {params.pfx} {input.bam}"
If one of the output files is not created by the rule, snakemake will remove all the output files for you, and throw an error.