From b2b8af792c8ee0e2fd6893da915b0ebda9517831 Mon Sep 17 00:00:00 2001
From: drpatelh <drhpatel@gmail.com>
Date: Wed, 5 Jun 2019 20:57:58 +0100
Subject: [PATCH 1/3] Add Zenodo doi

---
 README.md | 8 ++++++++
 1 file changed, 8 insertions(+)
 mode change 100755 => 100644 README.md

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).

From efaf08a5b0fa941787f08f93719e270e657d5547 Mon Sep 17 00:00:00 2001
From: Mingda Jin <jinmingda77@gmail.com>
Date: Fri, 27 Sep 2019 17:22:43 -0700
Subject: [PATCH 2/3] Use staged blacklist file in makeGenomeFilter

---
 main.nf | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/main.nf b/main.nf
index 5a732493..498501cb 100755
--- a/main.nf
+++ b/main.nf
@@ -451,6 +451,7 @@ 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 +462,7 @@ 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
     """

From 2ffcd46f59803fc7169967f5202c9d225ad72121 Mon Sep 17 00:00:00 2001
From: Mingda Jin <jinmingda77@gmail.com>
Date: Fri, 27 Sep 2019 18:19:25 -0700
Subject: [PATCH 3/3] Make sure channel variable blacklist is declared

Create an empty channel for blacklist when params.blacklist is false.
---
 main.nf | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/main.nf b/main.nf
index 498501cb..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()
 }
 
 ////////////////////////////////////////////////////