Does skip_preprocessing work (snakemake)?
I am trying to run a job skipping trimming and filtering since I already have clean reads. My config.imp.json file is attached. I run it with snakemake as:
CONFIGFILE="/home/jtamames/Huinay/IMP/config.imp.json" snakemake -s /home/jtamames/software/IMP/IMP/Snakefile --use-conda -p
and got this error:
Building DAG of jobs... MissingInputException in line 1 of /home/jtamames/software/IMP/IMP/rules/Preprocessing/trimming.rules: Missing input files for rule trimming: /home/my/Huinay/IMP/imp-db/adapters/adapters.done
Indeed the file /home/my/Huinay/IMP/imp-db/adapters/adapters.done is missing, but I set skip_preprocessing and preprocessing_filtering to "false" in the config file. Isn't that enough to skip the filtering step?