From 0ffa739cd06a555db388bf4338caff8e9e599d90 Mon Sep 17 00:00:00 2001
From: JoseEspinosa <kadomu@gmail.com>
Date: Tue, 14 Jul 2020 16:09:01 +0200
Subject: [PATCH] Changing fasta_sizes by chrom_sizes input path for genomecov

---
 software/bedtools/genomecov/main.nf  | 4 ++--
 software/bedtools/genomecov/meta.yml | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/software/bedtools/genomecov/main.nf b/software/bedtools/genomecov/main.nf
index 833f6e80..f8f354f2 100644
--- a/software/bedtools/genomecov/main.nf
+++ b/software/bedtools/genomecov/main.nf
@@ -5,7 +5,7 @@ process GENOMECOV {
 
     input:
         path (bam)
-        path (fasta_sizes)
+        path (chrom_sizes)
         val (genomecov_args)
 
     output:
@@ -13,6 +13,6 @@ process GENOMECOV {
 
     script:
     """
-    bedtools genomecov -ibam ${bam} -g ${fasta_sizes} ${genomecov_args}
+    bedtools genomecov -ibam ${bam} -g ${chrom_sizes} ${genomecov_args}
     """
 }
diff --git a/software/bedtools/genomecov/meta.yml b/software/bedtools/genomecov/meta.yml
index 0845cdb9..d06ecf9c 100644
--- a/software/bedtools/genomecov/meta.yml
+++ b/software/bedtools/genomecov/meta.yml
@@ -15,7 +15,7 @@ input:
             type: file
             description: Input genomic coordinates file
             pattern: "*.{bam}"
-        - fasta_sizes:
+        - chrom_sizes:
             type: file
               description: Genome chromosome sizes
               pattern: "*.{txt,sizes}"