Reverse is reserved for internal use

[blediro]

Hello,

I'm getting the following error after trying to run the snakemake script:

The flag 'directory' used in rule all is only valid for outputs, not inputs.
AttributeError in file /home/jcsm2010/scratch/jcsm2010/SnakeWRAP/Snakefile, line 87:
invalid name for input, output, wildcard, params or log: reverse is reserved for internal use
File "/home/jcsm2010/scratch/jcsm2010/SnakeWRAP/Snakefile", line 87, in

What can I do to resolve this issue?

[jkrapohl]

What commands/inputs are you using?

[blediro]

First I activated the metawrap environement "metawrap-env" and stacked on top of that the snakemake environment. Then, I'm executing the workflow as a one liner in a separate screen session with:

snakemake -p -s /home/jcsm2010/scratch/jcsm2010/SnakeWRAP/Snakefile --nolock --use-conda --configfile /home/jcsm2010/scratch/jcsm2010/SnakeWRAP/sample-config.yaml
--cluster 'qsub -l {resource_list} -N {job_name} -A {account} -m {mail_opt} -M {email} -V -o {log_out} -e {error_log}'

I had to define the parameters required by the job scheduler in both the config file and the snakemake script beforehand.

Now , as for the error I was able to solve it by changing all instances where "reverse" was used to something else. In my case I used "rev". I also had to make the read_qc_snakemake.sh script executable because it was giving me permission errors.