Update documentation and use GTF file.

README.md

@@ -73,6 +73,7 @@ $ git clone git@git.biohpc.swmed.edu:BICF/Astrocyte/chipseq_analysis.git
     9. Annotate all peaks using ChipSeeker
     10. Calculate Differential Binding Activity with DiffBind (If more than 1 rep in more than 1 experiment)
     11. Use MEME-ChIP to find motifs in original peaks
+    12. Plot enrichment of signal around TSS
 
 See [FLOWCHART](docs/flowchart.pdf)
 

docs/index.md

@@ -20,6 +20,7 @@ Report issues to the Bioinformatic Core Facility [BICF](mailto:BICF@UTSouthweste
     9. Annotate all peaks using ChipSeeker
     10. Calculate Differential Binding Activity with DiffBind (If more than 1 rep in more than 1 experiment)
     11. Use MEME-ChIP to find motifs in original peaks
+    12. Plot enrichment of signal around TSS
 
 
 ## Workflow Parameters

workflow/main.nf

@@ -488,6 +488,7 @@ process plotProfile {
   output:
 
   file '*.{png,gz}' into plotProfile
+  file gtf from gtfFile
 
   when: