MissingInputException

[LeilaKhajavi]

hello

running the following command resulted in the following error:

~/RIMA_pipeline$ snakemake -s RIMA.snakefile -np
Building DAG of jobs...
MissingInputException in line 96 of modules/mutation/mutation_cohort.snakefile:
Missing input files for rule fusion_plot:
analysis/batchremoval/tpm.genesymbol.batchremoved.csv

[ZHawul]

Hi LeilaKhajavi, I’m not part of the development team but I have also this same problem. At least for me, this is caused when the execution.yaml has the cohort runs set as true when the preprocessing steps have not already been run. I get around this by running just the preprocessing preprocess_individual and preprocess_cohort alone, i.e., the Individual runs and Cohort runs are all set to false. And then running the Individual runs and Cohort runs in a second run (I don’t change anything but set the job flags to true in the execution.yaml). If the analysis folder already has the pre-processed data, it skips the preprocessing steps and starts with the Individual runs. A bit of a pain to have to run the pipeline twice but at least it works.

[LeilaKhajavi]

Thank you!
I will try that 😊