See below, I fail to understand why my parameters par1 and par2 are the same in spite of the .split() function.
See this self contained example which is runnable.
Your will need to do "touch id1-one.input id2-two.input" in the working directory.
files=["id1-one", "id2-two"]
rule all:
input:
expand("{sample}.output",sample=files)
rule myrule:
params:
par1 = "{sample}",
par2 = "{sample}".split("-")
input:
i = "{sample}.input"
output:
o = "{sample}.output"
shell:
"./myprog -i ${input.i} -o {output.o} par1: {params.par1} par2: {params.par2}"
Output from running is:
$ snakemake -s small3.smk --cores 10 -n -p
Building DAG of jobs...
Job stats:
job count min threads max threads
------ ------- ------------- -------------
all 1 1 1
myrule 2 1 1
total 3 1 1
[Sat Dec 11 18:59:02 2021]
rule myrule:
input: id2-two.input
output: id2-two.output
jobid: 2
wildcards: sample=id2-two
resources: tmpdir=/var/folders/jb/b9y_67gx3v727w68k7mgrpdm0000gn/T
./myprog -i $id2-two.input -o id2-two.output par1: id2-two par2: id2-two
[Sat Dec 11 18:59:02 2021]
rule myrule:
input: id1-one.input
output: id1-one.output
jobid: 1
wildcards: sample=id1-one
resources: tmpdir=/var/folders/jb/b9y_67gx3v727w68k7mgrpdm0000gn/T
./myprog -i $id1-one.input -o id1-one.output par1: id1-one par2: id1-one
[Sat Dec 11 18:59:02 2021]
localrule all:
input: id1-one.output, id2-two.output
jobid: 0
resources: tmpdir=/var/folders/jb/b9y_67gx3v727w68k7mgrpdm0000gn/T
Job stats:
job count min threads max threads
------ ------- ------------- -------------
all 1 1 1
myrule 2 1 1
total 3 1 1
This was a dry-run (flag -n). The order of jobs does not reflect the order of execution.
You should use an input function inside params to get what you want:
rule myrule:
params:
params3 = lambda wildcards: wildcards.sample.split("-")
...
shell:
"par1: {params.par1} par2: {params.par2} par3: {params.par3} par3[0]: {params.par3[0]}"
Expands to, for id1-one:
par1: id1-one par2: id1-one par3: id1 one par3[0]: id1