IMPROVE: create rulegraph and full DAG in dot format

README.md

@@ -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)

Snakefile

@@ -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"

report/rulegraph.dot

+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"];
+	7 -> 0
+	8 -> 0
+	1 -> 0
+	2 -> 0
+	3 -> 0
+	5 -> 0
+	9 -> 0
+	4 -> 0
+	6 -> 0
+	2 -> 1
+	11 -> 2
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+	22 -> 27
+}