Move process containers to profile configs

workflow/conf/aws_ondemand.config

@@ -10,4 +10,26 @@ aws {
 process {
   executor = 'awsbatch'
   queue = 'highpriority-3278a8b0-1fc8-11ea-b1ac-021e2396e2cc'
+  
+  withLabel:checkDesignFile {
+    container = 'docker://bicf/python3:1.2'\
+  }
+  withLabel:untarBCL {
+    container = 'docker://bicf/bicfbase:1.3'\
+  }
+  withLabel:mkfastq {
+    container = 'docker://bicf/cellranger3.1.0:1.0'
+  }
+  withLabel:countDesign {
+    container = 'docker://bicf/bicfbase:1.3'
+  }
+  withLabel:fastqc {
+    module = ['fastqc/0.11.5', 'parallel']
+  }
+  withLabel:versions {
+    module = ['python/3.6.1-2-anaconda', 'cellranger/3.0.2', 'bcl2fastq/2.19.1', 'fastqc/0.11.5']
+  }
+  withLabel:multiqc {
+    container = 'docker://bicf/multiqc:1.4'
+  }
 }
\ No newline at end of file

workflow/conf/aws_spot.config

@@ -10,4 +10,26 @@ aws {
 process {
   executor = 'awsbatch'
   queue = 'default-3278a8b0-1fc8-11ea-b1ac-021e2396e2cc'
+
+  withLabel:checkDesignFile {
+    container = 'docker://bicf/python3:1.2'\
+  }
+  withLabel:untarBCL {
+    container = 'docker://bicf/bicfbase:1.3'\
+  }
+  withLabel:mkfastq {
+    container = 'docker://bicf/cellranger3.1.0:1.0'
+  }
+  withLabel:countDesign {
+    container = 'docker://bicf/bicfbase:1.3'
+  }
+  withLabel:fastqc {
+    module = ['fastqc/0.11.5', 'parallel']
+  }
+  withLabel:versions {
+    module = ['python/3.6.1-2-anaconda', 'cellranger/3.0.2', 'bcl2fastq/2.19.1', 'fastqc/0.11.5']
+  }
+  withLabel:multiqc {
+    container = 'docker://bicf/multiqc:1.4'
+  }
 }
\ No newline at end of file

workflow/conf/biohpc.config

@@ -3,26 +3,32 @@ process {
   queue = 'super'
   clusterOptions = '--hold'
 
-  // Process specific configuration
   withLabel:checkDesignFile {
+    container = 'docker://bicf/python3:1.2'
     executor = 'local'
   }
   withLabel:untarBCL {
+    container = 'docker://bicf/bicfbase:1.3'
     queue = 'super'
   }
   withLabel:mkfastq {
+    container = 'docker://bicf/cellranger3.1.0:1.0'
     queue = '128GB,256GB,256GBv1,384GB'
   }
   withLabel:countDesign {
+    container = 'docker://bicf/bicfbase:1.3'
     executor = 'local'
   }
   withLabel:fastqc {
+    module = ['fastqc/0.11.5', 'parallel']
     executor = 'super'
   }
   withLabel:versions {
+    module = ['python/3.6.1-2-anaconda', 'cellranger/3.0.2', 'bcl2fastq/2.19.1', 'fastqc/0.11.5']
     executor = 'local'
   }
   withLabel:multiqc {
+    container = 'docker://bicf/multiqc:1.4'
     executor = 'local'
   }
 }

workflow/conf/biohpc_local.config

 process {
   executor = 'local'
+
+  withLabel:checkDesignFile {
+    container = 'docker://bicf/python3:1.2'
+  }
+  withLabel:untarBCL {
+    container = 'docker://bicf/bicfbase:1.3'
+  }
+  withLabel:mkfastq {
+    container = 'docker://bicf/cellranger3.1.0:1.0'
+  }
+  withLabel:countDesign {
+    container = 'docker://bicf/bicfbase:1.3'
+  }
+  withLabel:fastqc {
+    module = ['fastqc/0.11.5', 'parallel']
+  }
+  withLabel:versions {
+    module = ['python/3.6.1-2-anaconda', 'cellranger/3.0.2', 'bcl2fastq/2.19.1', 'fastqc/0.11.5']
+  }
+  withLabel:multiqc {
+    container = 'docker://bicf/multiqc:1.4'
+  }
 }
 
 singularity {

workflow/nextflow.config

@@ -13,30 +13,6 @@ profiles {
   }
 }
 
-process {
-  withLabel:checkDesignFile {
-    container = 'docker://bicf/python3:1.2'
-  }
-  withLabel:untarBCL {
-    container = 'docker://bicf/bicfbase:1.3'
-  }
-  withLabel:mkfastq {
-    container = 'docker://bicf/cellranger3.1.0:1.0'
-  }
-  withLabel:countDesign {
-    container = 'docker://bicf/bicfbase:1.3'
-  }
-  withLabel:fastqc {
-    module = ['fastqc/0.11.5', 'parallel']
-  }
-  withLabel:versions {
-    module = ['python/3.6.1-2-anaconda', 'cellranger/3.0.2', 'bcl2fastq/2.19.1', 'fastqc/0.11.5']
-  }
-  withLabel:multiqc {
-    container = 'docker://bicf/multiqc:1.4'
-  }
-}
-
 trace {
   enabled = true
   file = 'pipeline_trace.txt'