chromosome breaks

tasks/Freebayes.wdl

@@ -15,7 +15,7 @@ task freebayes {
 		set -o pipefail
 		set -e	
 		nt=$(nproc)
-		freebayes -f ${ref_dir}/${fasta} --genotype-qualities --max-complex-gap ${half_read_length} ${chr_bam} > ${sample_name}_${chromosome}_fb.vcf
+		/opt/freebayes/bin/freebayes -f ${ref_dir}/${fasta} --genotype-qualities --max-complex-gap ${half_read_length} ${chr_bam} > ${sample_name}_${chromosome}_fb.vcf
 	>>>
 
 	runtime {

tasks/breakChromo.wdl

@@ -23,6 +23,6 @@ task breakChromo {
 	}
 	output {
 		File chr_bam = "${sample_name}_${chromosome}.bam"
-		File chr_bam_bai = "samtools index ${sample_name}_${chromosome}.bam.bai"
+		File chr_bam_bai = "${sample_name}_${chromosome}.bam.bai"
 	}
 }