From 24e74af8d6de847c13366d4ef698e389bbdbb46e Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Fri, 12 Feb 2021 12:25:35 -0600
Subject: [PATCH] Remove docker prefix

---
 nextflow.config | 52 ++++++++++++++++++++++++-------------------------
 rna-seq.nf      |  2 +-
 2 files changed, 27 insertions(+), 27 deletions(-)

diff --git a/nextflow.config b/nextflow.config
index afd3062..927e605 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -23,82 +23,82 @@ profiles {
 
 process {
   withName:getBag {
-    container = 'docker://gudmaprbk/deriva1.4:1.0.0'
+    container = 'gudmaprbk/deriva1.4:1.0.0'
   }
   withName:getData {
-    container = 'docker://gudmaprbk/deriva1.4:1.0.0'
+    container = 'gudmaprbk/deriva1.4:1.0.0'
   }
   withName:parseMetadata {
-    container = 'docker://gudmaprbk/python3:1.0.0'
+    container = 'gudmaprbk/python3:1.0.0'
   }
   withName:trimData {
-    container = 'docker://gudmaprbk/trimgalore0.6.5:1.0.0'
+    container = 'gudmaprbk/trimgalore0.6.5:1.0.0'
   }
   withName:getRefInfer {
-    container = 'docker://gudmaprbk/deriva1.4:1.0.0'
+    container = 'gudmaprbk/deriva1.4:1.0.0'
   }
   withName:downsampleData {
-    container = 'docker://gudmaprbk/seqtk1.3:1.0.0'
+    container = 'gudmaprbk/seqtk1.3:1.0.0'
   }
   withName:alignSampleData {
-    container = 'docker://gudmaprbk/hisat2.2.1:1.0.0'
+    container = 'gudmaprbk/hisat2.2.1:1.0.0'
   }
   withName:inferMetadata {
-    container = 'docker://gudmaprbk/rseqc4.0.0:1.0.0'
+    container = 'gudmaprbk/rseqc4.0.0:1.0.0'
   }
   withName:checkMetadata {
-    container = 'docker://gudmaprbk/gudmap-rbk_base:1.0.0'
+    container = 'gudmaprbk/gudmap-rbk_base:1.0.0'
   }
   withName:getRef {
-    container = 'docker://gudmaprbk/deriva1.4:1.0.0'
+    container = 'gudmaprbk/deriva1.4:1.0.0'
   }
   withName:alignData {
-    container = 'docker://gudmaprbk/hisat2.2.1:1.0.0'
+    container = 'gudmaprbk/hisat2.2.1:1.0.0'
   }
   withName:dedupData {
-    container = 'docker://gudmaprbk/picard2.23.9:1.0.0'
+    container = 'gudmaprbk/picard2.23.9:1.0.0'
   }
   withName:countData {
-    container = 'docker://gudmaprbk/subread2.0.1:1.0.0'
+    container = 'gudmaprbk/subread2.0.1:1.0.0'
   }
   withName:makeBigWig {
-    container = 'docker://gudmaprbk/deeptools3.5.0:1.0.0'
+    container = 'gudmaprbk/deeptools3.5.0:1.0.0'
   }
   withName:fastqc {
-    container = 'docker://gudmaprbk/fastqc0.11.9:1.0.0'
+    container = 'gudmaprbk/fastqc0.11.9:1.0.0'
   }
   withName:dataQC {
-    container = 'docker://gudmaprbk/rseqc4.0.0:1.0.0'
+    container = 'gudmaprbk/rseqc4.0.0:1.0.0'
   }
   withName:aggrQC {
-    container = 'docker://gudmaprbk/multiqc1.9:1.0.0'
+    container = 'gudmaprbk/multiqc1.9:1.0.0'
   }
   withName:uploadInputBag {
-    container = 'docker://gudmaprbk/deriva1.4:1.0.0'
+    container = 'gudmaprbk/deriva1.4:1.0.0'
   }
   withName:uploadExecutionRun {
-    container = 'docker://gudmaprbk/deriva1.4:1.0.0'
+    container = 'gudmaprbk/deriva1.4:1.0.0'
   }
   withName:uploadQC {
-    container = 'docker://gudmaprbk/deriva1.4:1.0.0'
+    container = 'gudmaprbk/deriva1.4:1.0.0'
   }
   withName:uploadProcessedFile {
-    container = 'docker://gudmaprbk/deriva1.4:1.0.0'
+    container = 'gudmaprbk/deriva1.4:1.0.0'
   }
   withName:uploadOutputBag {
-    container = 'docker://gudmaprbk/deriva1.4:1.0.0'
+    container = 'gudmaprbk/deriva1.4:1.0.0'
   }
   withName:finalizeExecutionRun {
-    container = 'docker://gudmaprbk/deriva1.4:1.0.0'
+    container = 'gudmaprbk/deriva1.4:1.0.0'
   }
   withName:failPreExecutionRun {
-    container = 'docker://gudmaprbk/deriva1.4:1.0.0'
+    container = 'gudmaprbk/deriva1.4:1.0.0'
   }
   withName:failExecutionRun {
-    container = 'docker://gudmaprbk/deriva1.4:1.0.0'
+    container = 'gudmaprbk/deriva1.4:1.0.0'
   }
   withName:uploadQC_fail {
-    container = 'docker://gudmaprbk/deriva1.4:1.0.0'
+    container = 'gudmaprbk/deriva1.4:1.0.0'
   }
 }
 
diff --git a/rna-seq.nf b/rna-seq.nf
index 264da73..c4e0e83 100644
--- a/rna-seq.nf
+++ b/rna-seq.nf
@@ -117,7 +117,7 @@ script_deleteEntry_uploadProcessedFile = Channel.fromPath("${baseDir}/scripts/de
  * trackStart: track start of pipeline
  */
 process trackStart {
-  container 'docker://gudmaprbk/gudmap-rbk_base:1.0.0'
+  container 'gudmaprbk/gudmap-rbk_base:1.0.0'
   script:
     """
     hostname
-- 
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