Snakemake input two variables and output one variable - snakemake

Question

I want to rename and move my fastq.gz files from these:
NAME-BOB_S1_L001_R1_001.fastq.gz
NAME-BOB_S1_L001_R2_001.fastq.gz
NAME-JOHN_S2_L001_R1_001.fastq.gz
NAME-JOHN_S2_L001_R2_001.fastq.gz
to these:
NAME_BOB/reads/NAME_BOB.R1.fastq.gz
NAME_BOB/reads/NAME_BOB.R2.fastq.gz
NAME_JOHN/reads/NAME_JOHN.R1.fastq.gz
NAME_JOHN/reads/NAME_JOHN.R2.fastq.gz
This is my code. The problem I have is the second variable S which I do not know how to specify in the code as I do not need it in my output filename.
workdir: "/path/to/workdir/"
DIR=["BOB","JOHN"]
S=["S1","S2"]
rule all:
input:
expand("NAME_{dir}/reads/NAME_{dir}.R1.fastq.gz", dir=DIR),
expand("NAME_{dir}/reads/NAME_{dir}.R2.fastq.gz", dir=DIR)
rule rename:
input:
fastq1=("fastq/NAME-{dir}_{s}_L001_R1_001.fastq.gz", zip, dir=DIR, s=S),
fastq2=("fastq/NAME-{dir}_{s}_L001_R2_001.fastq.gz", zip, dir=DIR, s=S)
output:
fastq1="NAME_{dir}/reads/NAME_{dir}.R1.fastq.gz",
fastq2="NAME_{dir}/reads/NAME_{dir}.R2.fastq.gz"
shell:
"""
mv {input.fastq1} {output.fastq1}
mv {input.fastq2} {output.fastq2}
"""

Answer 1

There are several problems in your code. First of all, the {dir} in your output and {dir} in your input are two different variables. Actually the {dir} in the output is a wildcard, while the {dir} in the input is a parameter for the expand function (moreover, you even forgot to call this function, and that is the second problem).
The third problem is that the shell section shall contain only a single command. You may try mv {input.fastq1} {output.fastq1}; mv {input.fastq2} {output.fastq2}, but this is not an idiomatic solution. Much better would be to create a rule that produces a single file, letting Snakemake to do the rest of the work.
Finally the S value fully depend on the DIR value, so it becomes a function of {dir}, and that can be solved with a lambda in input:
workdir: "/path/to/workdir/"
DIR=["BOB","JOHN"]
dir2s = {"BOB": "S1", "JOHN": "S2"}
rule all:
input:
expand("NAME_{dir}/reads/NAME_{dir}.{r}.fastq.gz", dir=DIR, r=["R1", "R2"])
rule rename:
input:
lambda wildcards:
"fastq/NAME-{{dir}}_{s}_L001_{{r}}_001.fastq.gz".format(s=dir2s[wildcards.dir])
output:
"NAME_{dir}/reads/NAME_{dir}.{r}.fastq.gz",
shell:
"""
mv {input} {output}
"""