Update containers to 2.0.0 and rejigger configs

workflow/configs/aws.config

@@ -14,24 +14,17 @@ process {
   memory = '1 GB'
 
   withName:checkDesignFile {
-    container = 'bicf/python3:1.3'
     cpus = 4
   }
   withName:mkfastq {
-    container = 'bicf/cellranger3.1.0:1.0'
     cpus = 6
     memory = '2 GB'
   }
   withName:fastqc {
-    container = 'bicf/fastqc:1.5'
     cpus = 30
     memory = '15 GB'
   }
   withName:versions {
-    container = 'bicf/python3:1.3'
     cpus = 6
   }
-  withName:multiqc {
-    container = 'bicf/multiqc:1.4'
-  }
 }

workflow/configs/biohpc.config

-process {
-  container = 'docker://bicf/bicfbase:2.0.0'
-
-  withName:checkDesignFile {
-    container = 'docker://bicf/python3:1.3'
-  }
-  withName:mkfastq {
-    container = 'docker://bicf/cellranger3.1.0:1.0'
-  }
-  withName:fastqc {
-    container = 'docker://bicf/fastqc:1.5'
-  }
-  withName:versions {
-    container = 'docker://bicf/python3:1.3'
-  }
-  withName:multiqc {
-    container = 'docker://bicf/multiqc:1.4'
-  }
-}
-
-singularity {
-  enabled = true
-  cacheDir = '/project/shared/bicf_workflow_ref/singularity_images/'
-}
-
 env {
   http_proxy = 'http://proxy.swmed.edu:3128'
   https_proxy = 'http://proxy.swmed.edu:3128'

workflow/nextflow.config

@@ -22,6 +22,32 @@ profiles {
   }
 }
 
+process {
+  withName:checkDesignFile {
+    container = 'docker://bicf/python3:2.0.0'
+  }
+  withName:untarBCL {
+    container = 'docker://bicf/bicfbase:2.0.0'
+  }
+  withName:mkfastq {
+    container = 'docker://bicf/cellranger3.1.0:2.0.0'
+  }
+  withName:fastqc {
+    container = 'docker://bicf/fastqc:2.0.0'
+  }
+  withName:versions {
+    container = 'docker://bicf/python3:2.0.0'
+  }
+  withName:multiqc {
+    container = 'docker://bicf/multiqc:2.0.0'
+  }
+}
+
+singularity {
+  enabled = true
+  cacheDir = '/project/shared/bicf_workflow_ref/singularity_images/'
+}
+
 trace {
   enabled = true
   file = 'pipeline_trace.txt'