Possible issue with file path in bgcflow\workflow\rules\common.smk

[MagnusHaahr]

We had issue with following line:

Step 4. Preparing list of final outputs...
 - Getting outputs for project: Lactobacillus_delbrueckii
WorkflowError in file /home/mhaahr/bgcflow/workflow/rules/common.smk, line 731:
Failed to open source file /home/mhaahr/bgcflow/workflow/../../workflow/rules.yaml
FileNotFoundError: [Errno 2] No such file or directory: '/home/mhaahr/bgcflow/workflow/../../workflow/rules.yaml'

Worked afrer updating from:
Line 731: with open(workflow.source_path(f"../../{rule_dict_path}"), "r") as file:

to:
Line 731: with open(workflow.source_path(f"../{rule_dict_path}"), "r") as file:

[alpole23]

ran into this same issue. your fix solved the problem. thanks!

[shuklagyanesh21]

At the first sight it seems to work. But does it really? Did it work for your own dataset?
I am getting a lot of "File Not Found Error" Especially when we try to build reports even if the files are processed and present in the interim folder, for some reason the summary df(s) are not being created for most rules in the tables folder (where the program looks for df(s) for building most reports).

How can such a issue be number #369 ? No one till now saw this wrong relative path calling issue which is present in plain sight? We are doing something incorrect I feel.

[MatissMaleckis]

Solved the problem after doing fresh install, thank you Magnus!

[chrisharper-stl]

Why hasn't this been addressed? All these tools were put together into an easy pipeline and people have been using it and publishing papers, but there's an error that prevents it from running properly because it references a directory outside of the bgcflow directory that doesn't exist? and the workaround is to fix the errors in the snakemake file yourself? Is that what everyone is doing? @shuklagyanesh21 Did you find a fix to this? I got the dry run to finish error free by copying /home/my_folder/bgcflow/workflow/rules.yaml to /home/my_folder/workflow/rules.yaml. I don't want to go through all the files to figure out which workaround is going to execute these pipelines properly and which are going to give me an error somewhere downstream. Can anyone provide some insight?

[georgiibondarev]

Changing Line 731 to with open(workflow.source_path(f"../{rule_dict_path}"), "r") as file: fixed this problem for me too. Thanks, Magnus!