rule not picked up by snakemake - snakemake

Question

I'm starting with snakemake. I managed to define some rules which I can run indepently, but not in a workflow. Maybe the issue is that they have unrelated inputs and outputs.
My current workflow is like this:
configfile: './config.yaml'
rule all:
input: dynamic("task/{job}/taskOutput.tab")
rule split_input:
input: "input_fasta/snp.fa"
output: dynamic("task/{job}/taskInput.fa")
shell:
"rm -Rf tasktmp task; \
mkdir tasktmp task; \
split -l 200 -d {input} ./tasktmp/; \
ls tasktmp | awk '{{print \"mkdir task/\"$0}}' | sh; \
ls tasktmp | awk '{{print \"mv ./tasktmp/\"$0\" ./task/\"$0\"/taskInput.fa\"}}' | sh"
rule task:
input: "task/{job}/taskInput.fa"
output: "task/{job}/taskOutput.tab"
shell: "cp {input} {output}"
rule make_parameter_file:
output:
"par/parameters.txt
shell:
"rm -Rf par;mkdir par; \
echo \"\
minimumFlankLength=5\n\
maximumFlankLength=200\n\
alignmentLengthDifference=2\
allowedMismatch=4\n\
allowedProxyMismatch=2\n\
allowedIndel=3\n\
ambiguitiesAsMatch=1\n\" \
> par/parameters.txt"
rule build_target:
input:
"./my_target"
output:
touch("build_target.done")
shell:
"build_target -template format_nt -source {input} -target my_target"
If I call this as such:
snakemake -p -s snakefile
The first three rules are being executed, the others not.
I can run the last rule by specifying it as an argument.
snakemake -p -s snakefile build_target
But I don't see how I can run all.
Thanks a lot for any suggestion on how to solve this.

Answer 1

By default snakemake executes only the first rule of a snakefile. Here it is rule all. In order to produce rule all's input dynamic("task/{job}/taskOutput.tab"), it needs to run the following two rules task and split_input, and so it does.
If you want the other rules to be run as well, you should put their output in rule all, eg.:
rule all:
input:
dynamic("task/{job}/taskOutput.tab"),
"par/parameters.txt",
"build_target.done"