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Commit 9c972d27 authored by Helene Rimbert's avatar Helene Rimbert
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IMPROVE: create rulegraph and full DAG in dot format

parent 2e4a5a8c
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1 merge request!7Missing conda rules
......@@ -192,11 +192,11 @@ You can generate the diagram of all the processes and dependancies of you analys
$ snakemake --dag |dot -T png > dag.png
```
This will generate a PNG file of your diagram.
![dag.png](report/dag.png)
![dag.svg](report/dag.svg)
If you simply want the global process of the pipeline, you may run:
```bash
$ snakemake --rulegraph |dot -T png > rulegraph.png
```
This will generate a PNG file of your diagram.
![rulegraph.png](report/rulegraph.png)
![rulegraph.svg](report/rulegraph.svg)
......@@ -18,16 +18,16 @@ rule all:
config['finalPrefix']+'_gmap_differentChrom.txt',
config['finalPrefix']+'_anchoringSummary.csv',
config['finalPrefix']+'_blatSummary.csv',
'report/dag.png',
'report/rulegraph.png'
'report/dag.dot',
'report/rulegraph.dot'
rule createDiagrams:
message: "Create dag and rulegraph of the pipeline"
output: dag='report/dag.png', rulegraphe='report/rulegraph.png'
output: dag='report/dag.dot', rulegraph='report/rulegraph.dot'
shell:
"""
snakemake --dag |dot -T png > {output.dag}
snakemake --rulegraph |dot -T png > {output.rulegraphe}
snakemake --dag > {output.dag}
snakemake --rulegraph > {output.rulegraph}
"""
include: "rules/preprocessISBP.smk"
......
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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 = "0.21 0.6 0.85", style="rounded"];
1[label = "renameGeneIds", color = "0.60 0.6 0.85", style="rounded"];
2[label = "concatAllChromResults", color = "0.16 0.6 0.85", style="rounded"];
3[label = "generateFastaSequencesHC", color = "0.44 0.6 0.85", style="rounded"];
4[label = "validateCdsHC", color = "0.37 0.6 0.85", style="rounded"];
5[label = "generateFastaSequencesLC", color = "0.34 0.6 0.85", style="rounded"];
6[label = "validateCdsLC", color = "0.23 0.6 0.85", style="rounded"];
7[label = "concatAnchoringSummary", color = "0.39 0.6 0.85", style="rounded"];
8[label = "concatblatSummary", color = "0.53 0.6 0.85", style="rounded"];
9[label = "createDiagrams", color = "0.18 0.6 0.85", style="rounded"];
10[label = "mergeFinalGff3", color = "0.46 0.6 0.85", style="rounded"];
11[label = "saveGmapWG", color = "0.48 0.6 0.85", style="rounded"];
12[label = "checkMissing", color = "0.25 0.6 0.85", style="rounded"];
13[label = "mapHomologousRegions", color = "0.30 0.6 0.85", style="rounded"];
14[label = "gtCleanBlatGff", color = "0.11 0.6 0.85", style="rounded"];
15[label = "recalcGmapRescue", color = "0.05 0.6 0.85", style="rounded"];
16[label = "gmapRescue", color = "0.32 0.6 0.85", style="rounded"];
17[label = "splitGffPerChrom", color = "0.07 0.6 0.85", style="rounded"];
18[label = "upstreamClosest", color = "0.62 0.6 0.85", style="rounded"];
19[label = "downstreamClosest", color = "0.28 0.6 0.85", style="rounded"];
20[label = "indexQuery", color = "0.14 0.6 0.85", style="rounded"];
21[label = "indexTarget", color = "0.02 0.6 0.85", style="rounded"];
22[label = "bam2bed", color = "0.41 0.6 0.85", style="rounded"];
23[label = "recalcBlatMapped", color = "0.55 0.6 0.85", style="rounded"];
24[label = "grepGffFeature", color = "0.64 0.6 0.85", style="rounded"];
25[label = "keepMappedOnSameChrom", color = "0.00 0.6 0.85", style="rounded"];
26[label = "filterBam", color = "0.51 0.6 0.85", style="rounded"];
27[label = "selectMappedISBP", color = "0.57 0.6 0.85", style="rounded"];
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}
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