Added container functionality

workflow/conf/biohpc.config

 process {
   executor = 'slurm'
-  queue='super'
+  queue = 'super'
 
   // Process specific configuration
-  withLabel:getData {
-    executor = 'super'
+  withName:getData {
+    container = 'docker://bicf/bdbag:1.0'
   }
 }
 
@@ -28,4 +28,19 @@ report {
 tower {
   accessToken = '3ade8f325d4855434b49aa387421a44c63e3360f'
   enabled = true
-}
\ No newline at end of file
+}
+
+singularity {
+  enabled = true
+  cacheDir = '/project/BICF/BICF_Core/s181706/github/gudmap/rna-seq/workflow/singularity'
+}
+
+env {
+  http_proxy = "http://proxy.swmed.edu:3128"
+  https_proxy = "http://proxy.swmed.edu:3128"
+  HTTP_PROXY = "http://proxy.swmed.edu:3128"
+  HTTPS_PROXY = "http://proxy.swmed.edu:3128"
+  all_proxy = "http://proxy.swmed.edu:3128"
+  ALL_PROXY = "http://proxy.swmed.edu:3128"
+}
+

workflow/rna-seq.nf

@@ -19,7 +19,7 @@ outDir = params.outDir
  */
  process getData {
      publishDir "${outDir}/temp/getData", mode: "symlink"
-     conda "${baseDir}/conf/conda.env.bdbag.yml"
+//     conda "${baseDir}/conf/conda.env.bdbag.yml"
 
      input:
         file bdbag
@@ -46,4 +46,4 @@ outDir = params.outDir
         sh ${baseDir}/scripts/renameFastq.sh \${study}
         echo LOG: fastq.gz files renamed to replicate RID
         """
- }
\ No newline at end of file
+ }