From fe2e27c7932e5cf7a6b270b3d66985b0eb7e62f2 Mon Sep 17 00:00:00 2001
From: sruthipsuresh <58604926+sruthipsuresh@users.noreply.github.com>
Date: Fri, 23 Oct 2020 08:14:40 -0500
Subject: [PATCH] Update main.nf

Updated bedtools module with updated container version and upstream/downstream values.
---
 software/bedtools/slopRefseq/main.nf | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/software/bedtools/slopRefseq/main.nf b/software/bedtools/slopRefseq/main.nf
index 9ec2eea2..fb643375 100644
--- a/software/bedtools/slopRefseq/main.nf
+++ b/software/bedtools/slopRefseq/main.nf
@@ -17,11 +17,11 @@ process BEDTOOLS_SLOPEREFSEQ {
     if (workflow.containerEngine == 'singularity' && !params.pull_docker_container) {
         container "https://depot.galaxyproject.org/singularity/bedtools:2.29.2--hc088bd4_0 "
     } else {
-        container "quay.io/biocontainers/bedtools:2.27.0--he513fc3"
+        container "quay.io/biocontainers/bedtools:2.29.2--hc088bd4_0"
     }
 
     input:
-        path(genome_chrom.sizes)
+        path sizes
         tuple val(meta), path(beds)
 
     output:
@@ -33,7 +33,7 @@ process BEDTOOLS_SLOPEREFSEQ {
         def beds_files = beds.sort()
         def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
         """
-        slopBed -i $beds -g ${genome_chrom.sizes} -l 1 -r 10 > {prefix}.sloprefseq.bed
+        slopBed -i $beds -g $sizes -l ${params.upstream} -r {params.downstream} > ${prefix}.sloprefseq.bed
         echo $VERSION > ${software}.version.txt
         """
-}
\ No newline at end of file
+}