Running cifiasm outside the repository directory

[schellt]

Hi Mo,
sorry for spamming issues.

1. Calling calN50.js
   When running the pipeline, I got the error:

ERROR: fail to open file 'scripts/calN50.js'.

This is probably caused by calling this script with a relative path. Since I am not running the pipeline in the same directory where the repository is located, this is most likely causing the issue.
For 3d-dna and juicer tools one can adjust the path in the config.yaml. Maybe you could either implement this and/or make calN50.js executable, so it can be recognized when the directory scripts is added to $PATH.

2. Relative output directory
   Furthermore, I saw that the results paths are sometimes relative too, when I leave the default (output_dir: results). Maybe you can get the absolute path of any user defined output_dir. E.g. for the pore-c workflow, the paths are absolute but index_fa and caln50 are relative.

3. Is it possible to define Snakefile on command line?
   Is it possible to run snakemake with a path to a Snakefile or does it has to be in the current directory? I am not very experienced with snakemake, sorry. If one could point to a certain Snakefile with and option, first one wouldn't need to copy that file before running cifiasm and second you could take this path and assume that 3d-dna and scripts is in the same location, unless the user defines something else.

Many thanks again for creating this pipeline.