diff --git a/README.md b/README.md
old mode 100755
new mode 100644
index 9c853408..1f34cf82
--- a/README.md
+++ b/README.md
@@ -6,6 +6,7 @@
 
 [![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg)](http://bioconda.github.io/)
 [![Docker](https://img.shields.io/docker/automated/nfcore/atacseq.svg)](https://hub.docker.com/r/nfcore/atacseq)
+[![DOI](https://zenodo.org/badge/156259074.svg)](https://zenodo.org/badge/latestdoi/156259074)
 
 ### Introduction
 
@@ -74,3 +75,10 @@ The pipeline was developed by [Harshil Patel](mailto:harshil.patel@crick.ac.uk).
 The [nf-core/rnaseq](https://github.com/nf-core/rnaseq) and [nf-core/chipseq](https://github.com/nf-core/chipseq) pipelines developed by Phil Ewels were initially used as a template for this pipeline. Many thanks to Phil for all of his help and advice, and the team at SciLifeLab.
 
 Many thanks to others who have helped out along the way too, including (but not limited to): [@apeltzer](https://github.com/apeltzer), [@sven1103](https://github.com/sven1103), [@MaxUlysse](https://github.com/MaxUlysse), [@micans](https://github.com/micans), [@pditommaso](https://github.com/pditommaso).
+
+## Citation
+
+If you use nf-core/atacseq for your analysis, please cite it using the following doi: [10.5281/zenodo.2634132](https://doi.org/10.5281/zenodo.2634132)
+
+You can cite the `nf-core` pre-print as follows:  
+Ewels PA, Peltzer A, Fillinger S, Alneberg JA, Patel H, Wilm A, Garcia MU, Di Tommaso P, Nahnsen S. **nf-core: Community curated bioinformatics pipelines**. *bioRxiv*. 2019. p. 610741. [doi: 10.1101/610741](https://www.biorxiv.org/content/10.1101/610741v1).
diff --git a/main.nf b/main.nf
index 5a732493..6c68c4c9 100755
--- a/main.nf
+++ b/main.nf
@@ -219,6 +219,8 @@ if (params.blacklist) {
     blacklist = Channel
         .fromPath(params.blacklist, checkIfExists: true)
         .ifEmpty { exit 1, "Blacklist file not found: ${params.blacklist}" }
+} else {
+    blacklist = Channel.empty()
 }
 
 ////////////////////////////////////////////////////
@@ -451,6 +453,7 @@ process makeGenomeFilter {
 
     input:
     file fasta from fasta_genome_filter
+    file blacklist from blacklist
 
     output:
     file "$fasta" into genome_fasta                 // FASTA FILE FOR IGV
@@ -461,7 +464,7 @@ process makeGenomeFilter {
                         genome_sizes_mrep_bigwig
 
     script:
-    blacklist_filter = params.blacklist ? "sortBed -i ${params.blacklist} -g ${fasta}.sizes | complementBed -i stdin -g ${fasta}.sizes" : "awk '{print \$1, '0' , \$2}' OFS='\t' ${fasta}.sizes"
+    blacklist_filter = params.blacklist ? "sortBed -i ${blacklist} -g ${fasta}.sizes | complementBed -i stdin -g ${fasta}.sizes" : "awk '{print \$1, '0' , \$2}' OFS='\t' ${fasta}.sizes"
     name_filter = params.mito_name ? "| awk '\$1 !~ /${params.mito_name}/ {print \$0}'": ""
     mito_filter = params.keepMito ? "" : name_filter
     """