Can I stop a rule in snakefile being parallel executed - snakemake

Question

I tried to concatenate files created via snakemake workflow as the last rule. To separate and identify the contents of each file, I echo each file name first in the shell as a separation tag (see the code below)
rule cat:
input:
expand('Analysis/typing/{sample}_type.txt', sample=samples)
output:
'Analysis/typing/Sum_type.txt'
shell:
'echo {input} >> {output} && cat {input} >> {output}'
I was looking for the result as this format:
file name of sample 1 content of sample 1 file name of sample
2 content of sample 2
instead I got this format:
file name of sample 1 file name of sample 2 ... content of sample 1
content of sample 2 ...
It seems snakemake execute echo command in parallel first then execute the cat command. What can I do the get the format I wanted?
Thanks

Answer 1

This looks more like a shell issue than a Snakemake issue.
If you want the file names and contents alternate, you can use a loop on the input files, as follows:
# Just an example:
samples = ["A", "B", "C"]
rule all:
input:
'Analysis/typing/Sum_type.txt'
rule cat:
input:
expand('Analysis/typing/{sample}_type.txt', sample=samples)
output:
'Analysis/typing/Sum_type.txt'
shell:
"""
for file in {input}
do
echo ${{file}} >> {output}
cat ${{file}} >> {output}
done
"""
(Double curly braces avoid the interpretation of the intended shell variable file as a thing that Snakemake/Python should "interpolate" when computing the string it passes to the shell.)

Answer 2

The output you get is consistent with the way bash works rather than with snakemake. Anyway, I think the snakemake way of doing it would be a rule to add the filename to the file content of each file and a rule to concatenate the output. E.g. (not checked for errors):
rule cat:
input:
'Analysis/typing/{sample}_type.txt',
output:
temp('Analysis/typing/{sample}_type.txt.out'),
shell:
r"""
echo {input} > {output}
cat {input} >> {output}
"""
rule cat_all:
input:
expand('Analysis/typing/{sample}_type.txt.out', sample=samples)
output:
'Analysis/typing/Sum_type.txt'
shell:
r"""
cat {input} > {output}
"""