
pairs = {"P1" : "P1", "P2" : "P2"}samples = { "sample1": "sample1", "sample2": "sample2"}wildcard_constraints: pair = "|".join(pairs), sample = "|".join(samples),rule all: input: expand("data/{sample}/{sample}_concatenated.txt", sample = samples)rule get_txt_files: output: "data/{sample}_{pair}.txt" shell: """ echo 1 > {output} """rule reorganise: input: expand("data/{{sample}}_{pair}.txt", \ pair=pairs) output: "data/{sample}/{sample}_{pair}.txt" shell: "mv {input} data/{wildcards.sample}/."rule concat: input: expand("data/{{sample}}/{{sample}}_{pair}.txt", \ pair=pairs) output: "data/{sample}/{sample}_concatenated.txt" shell: "cat {input} > {output}"