Merge branch 'revert-d5871e2a' into 'cellranger-4.0.0_ref-2020A'

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

See merge request !72

workflow/configs/biohpc.config

@@ -3,7 +3,3 @@ 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

@@ -63,7 +63,6 @@ references = Channel.fromPath("${baseDir}/../docs/references.md")
  */
 params.ci = false
 params.dev = false
-/*
 process trackStart {
   script:
   """
@@ -84,7 +83,7 @@ process trackStart {
   "https://xku43pcwnf.execute-api.us-east-1.amazonaws.com/ProdDeploy/pipeline-tracking"
   """
 }
-*/
+
 
 log.info """\
 ================================
@@ -107,6 +106,7 @@ Development     : ${params.dev}
 
 process checkDesignFile {
   tag "${name}"
+  module 'python/3.6.1-2-anaconda'
 
   input:
     file check_designScript
@@ -140,6 +140,7 @@ process checkDesignFile {
 
 process untarBCL {  
   tag "${tar.simpleName}"
+  module 'pigz/2.4'
 
   input:
     file untarBCLScript
@@ -166,6 +167,7 @@ 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
@@ -221,6 +223,7 @@ if (bclCount.value == 1) {
 
 process fastqc {
   tag "${bcl}"
+  module 'fastqc/0.11.5:parallel'
 
   input:
     file fastqcScript    
@@ -246,6 +249,7 @@ 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
@@ -275,6 +279,7 @@ 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

@@ -23,34 +23,6 @@ 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'