Calling mgefinder from a different workflow

[nongiga]

I created a snakemake workflow to make the necessary files and organize them for mgefinder, but I am having difficulties merging mgefinder, which has its own environment and configfile, as a part of my workflow

1. I tried using subworkflowbut then mgefinder runs first when I need it to run last
2. I was considering usinginclude but it prevents me from using a unique environment or config file.
3. I was considering creating a third workflow to call both subworkflows but didn't try it yet and it would complicate my debugging
4. I was considering modifying your original code to include 'env' in each call but it is (a) time-consuming and (b) not ideal in terms of best practices
5. Finally, I exported the mgefinder environment and made a rule that calls it. It works but my workflow sees it as one job and it is certainly far from best practices:

   rule mgefinder:
       input:
           lambda wildcards: 
               expand("mgefinder/{group}/00.bam/{sample2}.{sample1}.bam.bai",
                   sample1=GROUPS.get(int(wildcards.group)), 
                   sample2=GROUPS.get(int(wildcards.group)), 
                   allow_missing=True),
           lambda wildcards: 
               expand("mgefinder/{group}/00.{dirname}/{sample}.fna",
                   sample=GROUPS.get(int(wildcards.group)), 
                   dirname=["assembly","genome"],allow_missing=True),
       output:
           "mgefinder/{group}/dummy.txt"
       params:
           prefix="mgefinder/{group}/"
       conda:
           "database/mgefinder.yaml"
       shell:
           "mgefinder workflow denovo {params.prefix}; touch `{params.prefix}/dummy.txt"

I was wondering if you have any suggestions as to how to do it?

[durrantmm]

Hello, thank you for your question.

Have you considered adding in the additional rules to the existing mgefinder snakemake workflow, and then installing your software in the mgefinder conda environment?

[nongiga]

Great idea thank you! I didn't think about it before but in that case, actually, I could add the additional rules as a sub-workflow so they'd take only a few lines without interfering with your code, and will only be executed if the files weren't placed in the directory manually.