Update docs
I was testing Zarp by following README and discovered that several instructions should be corrected:
- The virtual environment
install/environment.ymlis not enough if the sample table contains files that should be concatenated. In this caseinstall/environment.dev.ymlis also required (unzippackage?). Possible solution: merging these two.ymlfiles into one. - In the section "Running the workflow on your own samples", item 4 the
snakemakecommand is described. There are two problems. First, the path to theSnakefileis wrong. It should be../../Snakefile. Second, for processing real samples on SLURM an additional option--latency-wait 60is required. With this option the system waits given seconds if an output file of a job is not present after the job finished. This helps if your filesystem suffers from latency (currently, it is the case).
Edited by Alex Kanitz