Snakemake version
9.3.3
Describe the bug
The output for rulegraph doesn't match that of mermaid-js, specifically the connection of rules by ids is incorrect.
Logs
Minimal example
In this example - the part I'm referring specifically to is the end section of sequence (id0 --> id0 and so on)
snakemake --dag
Output:
digraph snakemake_dag {
graph[bgcolor=white, margin=0];
node[shape=box, style=rounded, fontname=sans, fontsize=10, penwidth=2];
edge[penwidth=2, color=grey];
0[label = "all", color = "0.00 0.6 0.85", style="rounded"];
1[label = "Step3", color = "0.10 0.6 0.85", style="rounded"];
2[label = "Step2", color = "0.48 0.6 0.85", style="rounded"];
3[label = "Step1b", color = "0.29 0.6 0.85", style="rounded"];
4[label = "Step1c", color = "0.38 0.6 0.85", style="rounded"];
5[label = "Step4", color = "0.57 0.6 0.85", style="rounded"];
6[label = "Step1a", color = "0.19 0.6 0.85", style="rounded"];
4 -> 0
1 -> 0
2 -> 1
6 -> 2
3 -> 2
5 -> 4
1 -> 4
}
With mermaid (thanks btw for this!!)
snakemake --rulegraph mermaid-js
Output (incorrect):
flowchart TB
id0[all]
id1[Step3]
id2[Step2]
id3[Step1b]
id4[Step1c]
id5[Step4]
id6[Step1a]
style id0 fill:#D95757,stroke-width:2px,color:#333333
style id1 fill:#D9A157,stroke-width:2px,color:#333333
style id2 fill:#57D9C6,stroke-width:2px,color:#333333
style id3 fill:#7CD957,stroke-width:2px,color:#333333
style id4 fill:#57D97C,stroke-width:2px,color:#333333
style id5 fill:#57A1D9,stroke-width:2px,color:#333333
style id6 fill:#C6D957,stroke-width:2px,color:#333333
id0 --> id0
id0 --> id1
id1 --> id0
id2 --> id0
id2 --> id1
id4 --> id0
id4 --> id1
Additional context
Snakemake version
9.3.3
Describe the bug
The output for rulegraph doesn't match that of mermaid-js, specifically the connection of rules by ids is incorrect.
Logs
Minimal example
In this example - the part I'm referring specifically to is the end section of sequence (id0 --> id0 and so on)
snakemake --dagOutput:
With mermaid (thanks btw for this!!)
snakemake --rulegraph mermaid-jsOutput (incorrect):
Additional context