Merge branch 'containerize' into 'cellranger-4.0.0_ref-2020A'

# Conflicts:
#   workflow/main.nf
#   workflow/nextflow.config

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"
   """
 }
-
+*/
 
 log.info """\
 ================================
@@ -106,7 +107,6 @@ Development     : ${params.dev}
 
 process checkDesignFile {
   tag "${name}"
-  module 'python/3.6.1-2-anaconda'
 
   input:
     file check_designScript
@@ -140,7 +140,6 @@ process checkDesignFile {
 
 process untarBCL {  
   tag "${tar.simpleName}"
-  module 'pigz/2.4'
 
   input:
     file untarBCLScript
@@ -167,7 +166,6 @@ process mkfastq {
   tag "${bcl.simpleName}"
   publishDir "${outDir}/${task.process}", mode: 'copy', pattern: "{*/outs/**/*.fastq.gz}"
   queue '128GB,256GB,256GBv1,384GB'
-  module 'cellranger/4.0.0:bcl2fastq/2.19.1'
 
   input:
     file versions_cellrangerScript
@@ -223,7 +221,6 @@ if (bclCount.value == 1) {
 
 process fastqc {
   tag "${bcl}"
-  module 'fastqc/0.11.5:parallel'
 
   input:
     file fastqcScript    
@@ -249,7 +246,6 @@ process fastqc {
 
 process versions {
   tag "${name}"
-  module 'python/3.6.1-2-anaconda:cellranger/3.1.0:bcl2fastq/2.19.1:fastqc/0.11.5:pandoc/2.7'
 
   input:
   file versionsScript
@@ -279,7 +275,6 @@ process versions {
 process multiqc {
   tag "${name}"
   publishDir "${outDir}/${task.process}/${name}", mode: 'copy', pattern: "{multiqc*}"
-  module 'multiqc/1.7'
 
   input:
     file multiqcConf

workflow/nextflow.config

@@ -23,6 +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'