Remove docker prefix

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'
   }
 }
 

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