diff --git a/main.nf b/main.nf
index a57fe1ef38bef1d2b704d45dad9f1666976caac4..7eb43154af1206fab562a759ac27a87faacb86ed 100644
--- a/main.nf
+++ b/main.nf
@@ -223,10 +223,6 @@ else {
 // Resolutions for contact maps
 map_res = Channel.from( params.bin_size.tokenize(',') )
 
-// Stage config files
-ch_multiqc_config = Channel.fromPath(params.multiqc_config)
-ch_output_docs = Channel.fromPath("$baseDir/docs/output.md")
-
 /**********************************************************
  * SET UP LOGS
  */
diff --git a/nextflow.config b/nextflow.config
index 4ad6c94db6d7d348c3e615bff047118c7681ecc8..868ed5b19838b3b07de72db7b82df23e7d1def92 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -38,7 +38,6 @@ params {
 
   // Boilerplate options
   name = false
-  multiqc_config = "$baseDir/assets/multiqc_config.yaml"
   email = false
   email_on_fail = false
   max_multiqc_email_size = 25.MB