NEW step in the pipeline to generate output plots

Author: koszulordie

05_output_plots.nf

@@ -0,0 +1,64 @@
+SATURATION_OUT = Channel.fromPath("${OUTPUT}/saturation/prediction/*.model.*.features.*.prediction.tsv.gz")
+GENE_TTYPE_SATURATION_OUT = SATURATION_OUT.map{ it -> [it.baseName.split('\\.')[0], it.baseName.split('\\.')[2], it.baseName.split('\\.')[4]]}
+
+
+process Blueprints {
+    tag "Generate blueprints for gene=${gene} model=${ttype_model} features=${ttype_features}"
+    label "boostdm"
+    publishDir "${OUTPUT}/output_plots/blueprints", mode: 'copy'
+
+    input:
+        tuple val(gene), val(ttype_model), val(ttype_features) from GENE_TTYPE_SATURATION_OUT
+        
+    output:
+        path("${gene}.model.${ttype_model}.features.${ttype_features}.*") into OUT_BLUEPRINT
+
+    script:
+        
+        """
+        runner.sh output_plots/blueprint.py \
+                  --gene ${gene} \
+                  --ttmodel ${ttype_model} \
+                  --ttfeatures ${ttype_features}
+        """
+}
+
+
+process ClusteredBlueprints {
+    tag "Generate all blueprint stacks with hierarchical clustering"
+    label "boostdm"
+    publishDir "${OUTPUT}/output_plots/clustered_blueprints", mode: 'copy'
+
+    output:
+        path("*.clustered_blueprint.*") into OUT_CLUSTERED_BLUEPRINT
+
+    script:
+        
+        """
+        runner.sh output_plots/clustered_blueprint.py
+        """
+}
+
+
+TRAINING_OUT = Channel.fromPath("${OUTPUT}/training_meta/*/*.models.pickle.gz")
+GENE_TTYPE_TRAINING_OUT = TRAINING_OUT.map{ it -> [it.baseName.split('\\.')[0], it.getParent().baseName]}
+
+process DiscoveryBending {
+    tag "Generate inverse exponential fit with unique mutation count in subsamples for gene=${gene} ttype=${ttype}"
+    label "boostdm"
+    publishDir "${OUTPUT}/output_plots/discovery_bending", mode: 'copy'
+
+    input:
+        tuple val(gene), val(ttype) from GENE_TTYPE_TRAINING_OUT
+
+    output:
+        path("*.*.bending.*") into OUT_DISCOVERY_BENDING
+
+    script:
+        
+        """
+        runner.sh output_plots/discovery_plot.py \
+                  --gene ${gene} \
+                  --ttmodel ${ttype}
+        """
+}