Add basic multiqc process

README.md

-|*master*|*develop*|
-|:-:|:-:|
-|[![Build Status](https://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_mkfastq/badges/master/build.svg)](https://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_mkfastq/commits/master)|[![Build Status](https://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_mkfastq/badges/develop/build.svg)](https://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_mkfastq/commits/develop)|
-
 10x Genomics scRNA-Seq (cellranger) mkfastq Pipeline
 ========================================
 

workflow/conf/biohpc.config

@@ -15,6 +15,9 @@ process {
     module = ['cellranger/3.0.2', 'bcl2fastq/2.19.1']
     queue = '128GB,256GB,256GBv1,384GB'
   }
+  withLabel: multiqc {
+    module = ['multiqc/1.7']
+  }
 }
 
 

workflow/main.nf

@@ -67,7 +67,6 @@ process untarBCL {
   """
 }
 
-
 process mkfastq {
   tag "${bcl.baseName}"
   queue '128GB,256GB,256GBv1,384GB'
@@ -82,6 +81,7 @@ process mkfastq {
   output:
 
   file("**/outs/fastq_path/**/*") into fastqPaths
+  file("**/outs/fastq_path/Stats/Stats.json") into qc
 
   script:
 
@@ -93,3 +93,24 @@ process mkfastq {
   cellranger mkfastq --id="${bcl.baseName}" --run=$bcl --csv=$designPaths -r \$SLURM_CPUS_ON_NODE  -p \$SLURM_CPUS_ON_NODE  -w \$SLURM_CPUS_ON_NODE 
   """
 }
+
+process multiqc {
+  publishDir "$outDir/${task.process}", mode: 'copy'
+
+  input:
+
+  file qc
+
+  output:
+
+  file("*") into qcPaths
+
+  script:
+
+  """
+  hostname
+  ulimit -a
+  module load multiqc/1.7
+  multiqc Stats.json
+  """
+}