Include sample sheet in workdir

workflow/main.nf

@@ -27,6 +27,7 @@ process cr_count {
     input: 
         tuple val(sample), val(ref), val(expectCells), val(chemistry), val(introns), val(noBam)
         path(fastq)
+        path(sample_sheet)
         
     output:
         tuple val(sample), path("${task.index}_${sample}/outs/**")
@@ -80,8 +81,9 @@ process cr_count {
 workflow {
     // Parse sample sheet and run cellranger count
     fastq = channel.fromPath(params.fastq).collect()
+    sample_sheet = channel.fromPath(params.sample_sheet)
     input = channel.fromPath(params.sample_sheet) \
         | splitCsv(header: true) \
         | map{ row -> tuple( row.sample, row.reference, row.expectCells, row.chemistry, row.introns, row.noBam ) }
-    cr_count(input, fastq)
+    cr_count(input, fastq, sample_sheet)
 }