diff --git a/src/nf_modules/samtools/main.nf b/src/nf_modules/samtools/main.nf
index d44804b71bb4d0b3953ca1cf078e78882393d943..854c4f1d8c83f7010d3fea6a39e03afbc0c4c733 100755
--- a/src/nf_modules/samtools/main.nf
+++ b/src/nf_modules/samtools/main.nf
@@ -24,6 +24,7 @@ samtools sort -@ ${task.cpus} ${bam} -O BAM -o ${bam.simpleName}_sorted.bam
 
 params.start_position_counts_out = ""
 process start_position_counts {
+    container = "${container_url}"
     tag "${barcode}"
     label "big_mem_multi_cpus"
     publishDir "results/${params.start_position_counts_out}", mode: 'copy'
@@ -37,10 +38,9 @@ process start_position_counts {
     script:
 """
 mkdir ${barcode}
-cd ${barcode}/
-samtools view -F 260 ../${bam} |
+samtools view -F 260 ${bam} |
   cut -f 1,4 |
-  sort > ${barcode}_start_positions_counts.txt
+  sort > ${barcode}/${barcode}_start_positions_counts.txt
 """
 }