samtools location

README.md

@@ -10,6 +10,8 @@ Aligning RNAseq data to a reference genome is complicates by RNA splicing, [GATK
 
 Generate genome index files:
 
+The STAR you use 
+
 ```bash
 genomeDir=/path/to/GRCh38
 mkdir $genomeDir

tasks/indexBam.wdl

@@ -8,7 +8,7 @@ task indexBam {
 	command <<<
 		set -o pipefail
 		set -e	
-		samtools index ${sorted_bam}
+		/opt/conda/bin/samtools index ${sorted_bam}
 	>>>
 
 	runtime {