fix(HRD): path of sequenza.r

tasks/HRD.wdl

     set -e
     nt=$(nproc)
     
-    HRD_ANALYSIS_PATH="/cromwell_root/tmp"
-    mkdir $HRD_ANALYSIS_PATH
-    seqz=$HRD_ANALYSIS_PATH'/'${sample}'.seqz.gz'
-    small=$HRD_ANALYSIS_PATH'/'${sample}'.small.seqz.gz'
+    seqz=${sample}'.seqz.gz'
+    small=${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 $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
     sequenza-utils seqz_binning --seqz $seqz -w 50 -o $small
     
     # analysis in r
-    Rscript ~/sequenza.r $HRD_ANALYSIS_PATH ${sample}
+    Rscript /home/sequenza/sequenza.r '.' ${sample}
   >>>
   
   runtime {

tasks/MSIsensor.wdl

     nt=$(nproc)
     
     # MSI
-		mkdir -p /cromwell_root/tmp/${sample}
+		mkdir -p /cromwell_root/tmp/
     msisensor-pro scan -d ${ref_dir}/${fasta} -o reference.list
     if [ ${normal_bam} ]; then
       msisensor-pro msi -d reference.list -n ${normal_bam} -t ${tumor_bam} -o /cromwell_root/tmp/${sample}
       msisensor-pro pro -d ${baseline} -t ${tumor_bam} -o /cromwell_root/tmp/${sample}
     fi
     cp /cromwell_root/tmp/${sample} ${sample}.MSI.txt
-
-    # TMB
   >>>
   
   runtime {

tasks/Manta.wdl

     MANTA_ANALYSIS_PATH="/cromwell_root/tmp"
 		mkdir -p $MANTA_ANALYSIS_PATH
     
+    cp ${regions} my_baits.bed
+    bgzip -c my_baits.bed > my_baits.bed.gz
+    tabix -p bed my_baits.bed.gz
     # input files
     if [ ${normal_bam} ]; then
       INPUT="--normalBam ${normal_bam} --tumorBam ${tumor_bam}"
     # configManta
     $MANTA_INSTALL_PATH/bin/configManta.py \
     $INPUT \
-    --callRegions ${regions} --exome \
+    --callRegions my_baits.bed.gz --exome \
     --referenceFasta ${ref_dir}/${fasta} \
     --runDir $MANTA_ANALYSIS_PATH
     # runWorkflow