snakemake

How to use expand in snakemake when some particular combinations of wildcards are not desired?

被刻印的时光 ゝ 提交于 2019-11-28 14:28:22
Let's suppose that I have the following files, on which I want to apply some processing automatically using snakemake: test_input_C_1.txt test_input_B_2.txt test_input_A_2.txt test_input_A_1.txt The following snakefile uses expand to determine all the potential final results file: rule all: input: expand("test_output_{text}_{num}.txt", text=["A", "B", "C"], num=[1, 2]) rule make_output: input: "test_input_{text}_{num}.txt" output: "test_output_{text}_{num}.txt" shell: """ md5sum {input} > {output} """ Executing the above snakefile results in the following error: MissingInputException in line 4

How to use expand in snakemake when some particular combinations of wildcards are not desired?

為{幸葍}努か 提交于 2019-11-27 08:19:27
问题 Let's suppose that I have the following files, on which I want to apply some processing automatically using snakemake: test_input_C_1.txt test_input_B_2.txt test_input_A_2.txt test_input_A_1.txt The following snakefile uses expand to determine all the potential final results file: rule all: input: expand("test_output_{text}_{num}.txt", text=["A", "B", "C"], num=[1, 2]) rule make_output: input: "test_input_{text}_{num}.txt" output: "test_output_{text}_{num}.txt" shell: """ md5sum {input} >