Printing simplified DAG plot with snakemake
I have a long snakemake workflow processing 9 samples with many parallel rules. When I create a picture for the DAG with:
snakemake --forceall --dag | dot -Tpdf > dag.pdf
the resulting dag plot is huge and very redundant (and ugly because of complex node placement).
Is it possible to produce a canonical dag plot that will not show the 9 nodes for each task but only the main path through all steps?
I thought od simplifying my sample list to one sample but hope there is a better method without touching the snakefile (secret parameters?)
Thanks
snakemake
asked Nov 13 '18 at 14:06
splaisansplaisan
19712
add a comment |
I have a long snakemake workflow processing 9 samples with many parallel rules. When I create a picture for the DAG with:
snakemake --forceall --dag | dot -Tpdf > dag.pdf
the resulting dag plot is huge and very redundant (and ugly because of complex node placement).
Is it possible to produce a canonical dag plot that will not show the 9 nodes for each task but only the main path through all steps?
I thought od simplifying my sample list to one sample but hope there is a better method without touching the snakefile (secret parameters?)
Thanks
snakemake
asked Nov 13 '18 at 14:06
splaisansplaisan
19712
add a comment |
I have a long snakemake workflow processing 9 samples with many parallel rules. When I create a picture for the DAG with:
snakemake --forceall --dag | dot -Tpdf > dag.pdf
the resulting dag plot is huge and very redundant (and ugly because of complex node placement).
Is it possible to produce a canonical dag plot that will not show the 9 nodes for each task but only the main path through all steps?
I thought od simplifying my sample list to one sample but hope there is a better method without touching the snakefile (secret parameters?)
Thanks
snakemake
asked Nov 13 '18 at 14:06
splaisansplaisan
19712
I have a long snakemake workflow processing 9 samples with many parallel rules. When I create a picture for the DAG with:
snakemake --forceall --dag | dot -Tpdf > dag.pdf
the resulting dag plot is huge and very redundant (and ugly because of complex node placement).
Is it possible to produce a canonical dag plot that will not show the 9 nodes for each task but only the main path through all steps?
I thought od simplifying my sample list to one sample but hope there is a better method without touching the snakefile (secret parameters?)
Thanks
snakemake
snakemake
asked Nov 13 '18 at 14:06
splaisansplaisan
19712
asked Nov 13 '18 at 14:06
splaisansplaisan
19712
asked Nov 13 '18 at 14:06
splaisansplaisan
19712
asked Nov 13 '18 at 14:06
splaisansplaisan
19712
asked Nov 13 '18 at 14:06
splaisansplaisan
19712
19712
add a comment |
add a comment |
1 Answer
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Use the flag --rulegraph instead of --dag.
answered Nov 13 '18 at 14:12
The Unfun CatThe Unfun Cat
10.5k166691
never crossed this in my snakemake readings (obviously still insufficient). THANKS YOU
– splaisan
Nov 14 '18 at 14:05
add a comment |
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1 Answer
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1 Answer
1
active
oldest
votes
active
oldest
votes
active
oldest
votes
Use the flag --rulegraph instead of --dag.
answered Nov 13 '18 at 14:12
The Unfun CatThe Unfun Cat
10.5k166691
never crossed this in my snakemake readings (obviously still insufficient). THANKS YOU
– splaisan
Nov 14 '18 at 14:05
add a comment |
Use the flag --rulegraph instead of --dag.
answered Nov 13 '18 at 14:12
The Unfun CatThe Unfun Cat
10.5k166691
never crossed this in my snakemake readings (obviously still insufficient). THANKS YOU
– splaisan
Nov 14 '18 at 14:05
add a comment |
Use the flag --rulegraph instead of --dag.
answered Nov 13 '18 at 14:12
The Unfun CatThe Unfun Cat
10.5k166691
Use the flag --rulegraph instead of --dag.
answered Nov 13 '18 at 14:12
The Unfun CatThe Unfun Cat
10.5k166691
answered Nov 13 '18 at 14:12
The Unfun CatThe Unfun Cat
10.5k166691
answered Nov 13 '18 at 14:12
The Unfun CatThe Unfun Cat
10.5k166691
answered Nov 13 '18 at 14:12
The Unfun CatThe Unfun Cat
10.5k166691
10.5k166691
never crossed this in my snakemake readings (obviously still insufficient). THANKS YOU
– splaisan
Nov 14 '18 at 14:05
add a comment |
never crossed this in my snakemake readings (obviously still insufficient). THANKS YOU
– splaisan
Nov 14 '18 at 14:05
never crossed this in my snakemake readings (obviously still insufficient). THANKS YOU
– splaisan
Nov 14 '18 at 14:05
never crossed this in my snakemake readings (obviously still insufficient). THANKS YOU
– splaisan
Nov 14 '18 at 14:05
add a comment |
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