Tag: wildcard-expansion

Is there a function in snakemake to make the list of output dependent on the arguments passed into the shell command

directed-acyclic-graphs python snakemake wildcard-expansion

I have a snakemake rule that calls a python program, the output of the python program is dependent on the arguments passed. I would like to make snakemake aware of the differences between the expected output when a certain parameter is passed (Boolean) or not passed. My current solution is to create a list of output list_phen_gen_output dependent on the

Wrong snakemake glob_wilcards and wildcard_constraints

glob python snakemake wildcard-expansion

Within my snakemake pipeline I’m trying to retrieve the correct wildcards. I’ve looked into wildcard_constraints and this post and this post, however I can’t figure out the exact solution. Here’s an example of file names within 2 datasets. 1 dataset contains paired mouse RNAseq read files and another dataset contains human paired RNAseq read files. “Mus_musculus” dataset is “PRJNA362883_GSE93946_SRP097621” with

How to use wildcards in keyword wildcard_constraints

python snakemake wildcard wildcard-expansion

For example, I have the following wildcards. I am trying to contrain my dataset with my group. for example, I want to create A1/file.A.txt A2/file.A.txt A3/file.A.txt B1/file.B.txt … I wrote a following rule hoping to make that possible oops, I got the error It seems like that the {group} is regarded as a list to pass in the keywords wildcard_constraints.