fix: custom variables

tasks/AnnotSV.wdl

@@ -15,9 +15,9 @@ task AnnotSV {
     
     export ANNOTSV=/opt/AnnotSV
     if [ ${somatic_vcf} ]; then
-      ${ANNOTSV}/bin/AnnotSV -SVinputFile ${somatic_vcf} -outputFile ${sample}.somatic.SV.annotated.tsv -genomeBuild GRCh38 -annotationsDir ${annotsv_database}
+      $ANNOTSV/bin/AnnotSV -SVinputFile ${somatic_vcf} -outputFile ${sample}.somatic.SV.annotated.tsv -genomeBuild GRCh38 -annotationsDir ${annotsv_database}
     else
-      ${ANNOTSV}/bin/AnnotSV -SVinputFile ${germline_vcf} -outputFile ${sample}.germline.SV.annotated.tsv -genomeBuild GRCh38 -annotationsDir ${annotsv_database}
+      $ANNOTSV/bin/AnnotSV -SVinputFile ${germline_vcf} -outputFile ${sample}.germline.SV.annotated.tsv -genomeBuild GRCh38 -annotationsDir ${annotsv_database}
     fi
   >>>
   

tasks/CNVkit.wdl

@@ -18,8 +18,9 @@ task CNVkit {
     set -e
     nt=$(nproc)
     
-    mkdir -p /cromwell_root/tmp/cnvkit
-    cd /cromwell_root/tmp/cnvkit
+    CNV_ANALYSIS_PATH=/cromwell_root/tmp/cnvkit
+    mkdir -p $CNV_ANALYSIS_PATH
+    cd $CNV_ANALYSIS_PATH
     
     cnvkit.py access ${ref_dir}/${fasta} -o access.bed
     # Prepare the target bed

tasks/HRD.wdl

@@ -17,16 +17,16 @@ task HRD {
     set -e
     nt=$(nproc)
     
-    output_dir="/cromwell_root/tmp"
-    mkdir ${output_dir}
-    seqz=${output_dir}'/'${sample}'.seqz.gz'
-    small=${output_dir}'/'${sample}'.small.seqz.gz'
+    HRD_ANALYSIS_PATH="/cromwell_root/tmp"
+    mkdir $HRD_ANALYSIS_PATH
+    seqz=$HRD_ANALYSIS_PATH'/'${sample}'.seqz.gz'
+    small=$HRD_ANALYSIS_PATH'/'${sample}'.small.seqz.gz'
     
     # bam2seqz
     sequenza-utils bam2seqz -gc ${gc} --fasta ${ref_dir}/${fasta} -n ${normal_bam} -t ${tumor_bam} -o $seqz -C chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY --parallel 24
     
     # merge and remove
-    cd ${output_dir}
+    cd $HRD_ANALYSIS_PATH
     zcat ${sample}_*.seqz.gz | awk '{if (NR == 1 || (NR != 1 && $1 != "chromosome")) {print $0}}' | bgzip > $seqz
     tabix -f -s 1 -b 2 -e 2 -S 1 $seqz
     rm ${sample}_*.seqz.gz; rm ${sample}_*.seqz.gz.tbi
@@ -35,7 +35,7 @@ task HRD {
     sequenza-utils seqz_binning --seqz $seqz -w 50 -o $small
     
     # analysis in r
-    Rscript ~/sequenza.r ${output_dir} ${sample}
+    Rscript ~/sequenza.r $HRD_ANALYSIS_PATH ${sample}
   >>>
   
   runtime {