Improve input file import of fastqc process

workflow/conf/biohpc.config

@@ -15,8 +15,13 @@ process {
     module = ['cellranger/3.0.2', 'bcl2fastq/2.19.1']
     queue = '128GB,256GB,256GBv1,384GB'
   }
+  withLabel: fastqc {
+    module = ['fastqc/0.11.5', 'parallel']
+    executor = 'local'
+  }
   withLabel: multiqc {
     module = ['multiqc/1.7']
+    executor = 'local'
   }
 }
 

workflow/main.nf

@@ -80,7 +80,8 @@ process mkfastq {
 
   output:
 
-  file("**/outs/fastq_path/**/*") into fastqPaths
+  file("**/outs/fastq_path/**/*") into mkfastqPaths
+  file("**/outs/**/*.fastq.gz") into fastqPaths
   file("**/outs/fastq_path/Stats/Stats.json") into bqcPaths
 
   script:
@@ -99,7 +100,7 @@ process fastqc {
   publishDir "$outDir/${task.process}", mode: 'copy'
 
   input:
-  file("outs/fastq_path/*/*") from fastqPaths
+  file fastqPaths
 
   output:
 

workflow/scripts/fastqc.sh

 #!/bin/bash
 
 find . -name '*.fastq.gz' | awk '{printf("fastqc \"%s\"\n", $0)}' | parallel -j 25 --verbose
-find . -name '*fastqc.*' | xargs -I '{}' mv '{}' ./
+#find . -name '*fastqc.*' | xargs -I '{}' mv '{}' ./