recontaineraize

workflow/configs/biohpc.config

@@ -3,3 +3,7 @@ env {
   https_proxy = 'http://proxy.swmed.edu:3128'
   all_proxy = 'http://proxy.swmed.edu:3128'
 }
+
+singularity {
+  cacheDir = '/project/shared/bicf_workflow_ref/singularity_images/'
+}

workflow/main.nf

@@ -63,6 +63,7 @@ references = Channel.fromPath("${baseDir}/../docs/references.md")
  */
 params.ci = false
 params.dev = false
+/*
 process trackStart {
   script:
   """
@@ -83,7 +84,7 @@ process trackStart {
   "https://xku43pcwnf.execute-api.us-east-1.amazonaws.com/ProdDeploy/pipeline-tracking"
   """
 }
-
+*/
 
 process checkDesignFile {
 

workflow/nextflow.config

 profiles {
   standard {
     includeConfig 'configs/biohpc.config'
+    includeConfig 'configs/cluster.config'
   }
   biohpc {
     includeConfig 'configs/biohpc.config'
@@ -22,6 +23,34 @@ profiles {
   }
 }
 
+process {
+  withName:trackStart {
+    container = 'docker://bicf/bicfbase:2.0.0'
+  }
+  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
+}
+
 trace {
   enabled = true
   file = 'pipeline_trace.txt'