Add plotHeatmap

nf-core · Jun 2, 2020 · 23cc664 · 23cc664
1 parent a7fc1ed
commit 23cc664
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Showing 2 changed files with 6 additions and 2 deletions.
diff --git a/docs/output.md b/docs/output.md
@@ -151,7 +151,7 @@ The library-level alignments associated with the same sample are merged and subs
     * `bwa/mergedLibrary/deepTools/plotFingerprint/`  
       * Output files: `*.plotFingerprint.pdf`, `*.plotFingerprint.qcmetrics.txt`, `*.plotFingerprint.raw.txt`
     * `bwa/mergedLibrary/deepTools/plotProfile/`  
-      * Output files: `*.computeMatrix.mat.gz`, `*.computeMatrix.vals.mat.tab`, `*.plotProfile.pdf`, `*.plotProfile.tab`.
+      * Output files: `*.computeMatrix.mat.gz`, `*.computeMatrix.vals.mat.tab`, `*.plotProfile.pdf`, `*.plotProfile.tab`, `*.plotHeatmap.pdf`, `*.plotHeatmap.mat.tab`.
 
 4. **Call peaks**
 

diff --git a/main.nf b/main.nf
@@ -969,7 +969,7 @@ process BIGWIG {
 }
 
 /*
- * STEP 5.4: Generate gene body coverage plot with deepTools plotProfile
+ * STEP 5.4: Generate gene body coverage plot with deepTools plotProfile and plotHeatmap
  */
 process PLOTPROFILE {
     tag "$name"
@@ -1004,6 +1004,10 @@ process PLOTPROFILE {
     plotProfile --matrixFile ${name}.computeMatrix.mat.gz \\
         --outFileName ${name}.plotProfile.pdf \\
         --outFileNameData ${name}.plotProfile.tab
+
+    plotHeatmap --matrixFile ${name}.computeMatrix.mat.gz \\
+        --outFileName ${name}.plotHeatmap.pdf \\
+        --outFileNameMatrix ${name}.plotHeatmap.mat.tab
     """
 }