Rewrite container image references in the workflow config files to use the...

Rewrite container image references in the workflow config files to use the official container registry.

astrocyte_pkg.yml

@@ -63,10 +63,10 @@ workflow_modules:
 # Such as, "docker://", "shub://", "library://", etc. We encourage you to use the GitLab
 # container registry of BioHPC to save and manage your container images.
 workflow_containers:
-  - docker://git.biohpc.swmed.edu:5050/s219741/chipseq-analysis-containerized/r:3.3.2
-  - docker://git.biohpc.swmed.edu:5050/s219741/chipseq-analysis-containerized/python:3.6.1
-  - docker://git.biohpc.swmed.edu:5050/s219741/chipseq-analysis-containerized/chipseq:1.0.0
-  - docker://git.biohpc.swmed.edu:5050/s219741/chipseq-analysis-containerized/motif-search:meme-5.5.4
+  - docker://git.biohpc.swmed.edu/astrocyte/workflows/bicf/chipseq_analysis/r:3.3.2
+  - docker://git.biohpc.swmed.edu/astrocyte/workflows/bicf/chipseq_analysis/python:3.6.1
+  - docker://git.biohpc.swmed.edu/astrocyte/workflows/bicf/chipseq_analysis/chipseq:1.0.0
+  - docker://git.biohpc.swmed.edu/astrocyte/workflows/bicf/chipseq_analysis/motif-search:meme-5.5.4
 
 # A list of parameters used by the workflow, defining how to present them,
 # options etc in the web interface. For each parameter:

workflow/configs/biohpc.config

@@ -20,70 +20,70 @@ process {
   }
 
   withName: checkDesignFile {
-    container = 'docker://git.biohpc.swmed.edu:5050/s219741/chipseq-analysis-containerized/python:3.6.1'
+    container = 'docker://git.biohpc.swmed.edu/astrocyte/workflows/bicf/chipseq_analysis/python:3.6.1'
     executor = 'local'
   }
   withName: trimReads {
-    container = 'docker://git.biohpc.swmed.edu:5050/s219741/chipseq-analysis-containerized/chipseq:1.0.0'
+    container = 'docker://git.biohpc.swmed.edu/astrocyte/workflows/bicf/chipseq_analysis/chipseq:1.0.0'
     cpus = 32
   }
   withName: alignReads{
-    container = 'docker://git.biohpc.swmed.edu:5050/s219741/chipseq-analysis-containerized/chipseq:1.0.0'
+    container = 'docker://git.biohpc.swmed.edu/astrocyte/workflows/bicf/chipseq_analysis/chipseq:1.0.0'
     queue = '128GB,256GB,256GBv1'
     cpus = 32
   }
   withName: filterReads{
-    container = 'docker://git.biohpc.swmed.edu:5050/s219741/chipseq-analysis-containerized/chipseq:1.0.0'
+    container = 'docker://git.biohpc.swmed.edu/astrocyte/workflows/bicf/chipseq_analysis/chipseq:1.0.0'
     queue = '128GB,256GB,256GBv1'
   }
   withName: experimentQC {
-    container = 'docker://git.biohpc.swmed.edu:5050/s219741/chipseq-analysis-containerized/chipseq:1.0.0'
+    container = 'docker://git.biohpc.swmed.edu/astrocyte/workflows/bicf/chipseq_analysis/chipseq:1.0.0'
     queue = '128GB,256GB,256GBv1'
   }
   withName: convertReads {
-    container = 'docker://git.biohpc.swmed.edu:5050/s219741/chipseq-analysis-containerized/chipseq:1.0.0'
+    container = 'docker://git.biohpc.swmed.edu/astrocyte/workflows/bicf/chipseq_analysis/chipseq:1.0.0'
     queue = '128GB,256GB,256GBv1'
   }
   withName: crossReads {
-    container = 'docker://git.biohpc.swmed.edu:5050/s219741/chipseq-analysis-containerized/chipseq:1.0.0'
+    container = 'docker://git.biohpc.swmed.edu/astrocyte/workflows/bicf/chipseq_analysis/chipseq:1.0.0'
     cpus = 32
   }
   withName: defineExpDesignFiles {
-    container = 'docker://git.biohpc.swmed.edu:5050/s219741/chipseq-analysis-containerized/python:3.6.1'
+    container = 'docker://git.biohpc.swmed.edu/astrocyte/workflows/bicf/chipseq_analysis/python:3.6.1'
     executor = 'local'
   }
   withName: poolAndPsuedoReads {
-    container = 'docker://git.biohpc.swmed.edu:5050/s219741/chipseq-analysis-containerized/python:3.6.1'
+    container = 'docker://git.biohpc.swmed.edu/astrocyte/workflows/bicf/chipseq_analysis/python:3.6.1'
     executor = 'local'
   }
   withName: callPeaksMACS {
-    container = 'docker://git.biohpc.swmed.edu:5050/s219741/chipseq-analysis-containerized/chipseq:1.0.0'
+    container = 'docker://git.biohpc.swmed.edu/astrocyte/workflows/bicf/chipseq_analysis/chipseq:1.0.0'
     queue = '128GB,256GB,256GBv1'
   }
   withName: plotProfile {
-    container = 'docker://git.biohpc.swmed.edu:5050/s219741/chipseq-analysis-containerized/chipseq:1.0.0'
+    container = 'docker://git.biohpc.swmed.edu/astrocyte/workflows/bicf/chipseq_analysis/chipseq:1.0.0'
     queue = '128GB,256GB,256GBv1'
     cpus = 32
   }
   withName: consensusPeaks {
-    container = 'docker://git.biohpc.swmed.edu:5050/s219741/chipseq-analysis-containerized/chipseq:1.0.0'
+    container = 'docker://git.biohpc.swmed.edu/astrocyte/workflows/bicf/chipseq_analysis/chipseq:1.0.0'
     executor = 'local'
   }
   withName: peakAnnotation {
-    container = 'docker://git.biohpc.swmed.edu:5050/s219741/chipseq-analysis-containerized/r:3.3.2'
+    container = 'docker://git.biohpc.swmed.edu/astrocyte/workflows/bicf/chipseq_analysis/r:3.3.2'
     executor = 'local'
   }
   withName: diffPeaks {
-    container = 'docker://git.biohpc.swmed.edu:5050/s219741/chipseq-analysis-containerized/r:3.3.2'
+    container = 'docker://git.biohpc.swmed.edu/astrocyte/workflows/bicf/chipseq_analysis/r:3.3.2'
     cpus = 32
   }
   withName: motifSearch {
     executor = 'local'
-    container = 'docker://git.biohpc.swmed.edu:5050/s219741/chipseq-analysis-containerized/motif-search:meme-5.5.4'
+    container = 'docker://git.biohpc.swmed.edu/astrocyte/workflows/bicf/chipseq_analysis/motif-search:meme-5.5.4'
     //cpus = 32
   }
   withName: multiqcReport {
-    container = 'docker://git.biohpc.swmed.edu:5050/s219741/chipseq-analysis-containerized/chipseq:1.0.0'
+    container = 'docker://git.biohpc.swmed.edu/astrocyte/workflows/bicf/chipseq_analysis/chipseq:1.0.0'
     executor = 'local'
   }
 }