Add inital output bag creation

workflow/conf/aws.config

@@ -80,4 +80,8 @@ process {
     cpus = 2
     memory = '1 GB'
   }
+  withName: outputBag {
+    cpus = 1
+    memory = '1 GB'
+  }
 }

workflow/conf/biohpc.config

@@ -54,6 +54,9 @@ process {
   withName: aggrQC {
     executor = 'local'
   }
+  withName: outputBag {
+    executor = 'local'
+  }
 }
 
 singularity {

workflow/nextflow.config

@@ -67,6 +67,9 @@ process {
   withName: aggrQC {
     container = 'bicf/multiqc1.8:2.0.1_indev'
   }
+  withName:outputBag {
+    container = 'bicf/gudmaprbkfilexfer:2.0.1_indev'
+  }
 }
 
 trace {
@@ -94,6 +97,6 @@ manifest {
   homePage = 'https://git.biohpc.swmed.edu/gudmap_rbk/rna-seq'
   description = 'This pipeline was created to be a standard mRNA-sequencing analysis pipeline which integrates with the GUDMAP and RBK consortium data-hub.'
   mainScript = 'rna-seq.nf'
-  version = 'v0.0.1'
+  version = 'v0.0.2_indev'
   nextflowVersion = '>=19.09.0'
 }

workflow/rna-seq.nf

@@ -1058,4 +1058,28 @@ process aggrQC {
     multiqc -c ${multiqcConfig} . -n ${repRID}.multiqc.html
     cp ${repRID}.multiqc_data/multiqc_data.json ${repRID}.multiqc_data.json
     """
-}
\ No newline at end of file
+}
+
+/*
+ *ouputBag: create ouputBag
+*/
+process outputBag {
+  tag "${repRID}"
+  publishDir "${outDir}/outputBag", mode: 'copy', pattern: "Replicate_${repRID}.outputBag.zip"
+  
+  input:
+    path multiqc
+    path multiqcJSON
+  
+  output:
+    path ("Replicate_*.zip") into outputBag
+
+  script:
+  """
+  mkdir Replicate_${repRID}.outputBag
+  cp ${multiqc} Replicate_${repRID}.outputBag
+  cp ${multiqcJSON} Replicate_${repRID}.outputBag
+  bdbag Replicate_${repRID}.outputBag --archiver zip
+  """
+}
+