Merge branch 'develop' into feature/upgrade_nextflow

UMCUGenetics · Aug 8, 2023 · 841c1db · 841c1db
2 parents b9cc20a + 320a36e
commit 841c1db
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Showing 36 changed files with 138 additions and 62 deletions.
diff --git a/GATK/3.8-1-0-gf15c1c3ef/BaseRecalibrator.nf b/GATK/3.8-1-0-gf15c1c3ef/BaseRecalibrator.nf
@@ -13,15 +13,15 @@ process BaseRecalibrator {
 
     script:
         """
-        java -Xmx${task.memory.toGiga()-4}G -jar $params.gatk_path -T BaseRecalibrator \
+        java -Xmx${task.memory.toGiga()-4}G -Djava.io.tmpdir=\$TMPDIR -jar $params.gatk_path -T BaseRecalibrator \
         --num_cpu_threads_per_data_thread ${task.cpus} \
         --reference_sequence ${params.genome} \
         --input_file ${bam_file} \
         --intervals ${chr} \
         --out ${bam_file.baseName}.bqsr.${chr}.table \
         ${params.optional_bqsr}
 
-        java -Xmx${task.memory.toGiga()-4}G -jar ${params.gatk_path} -T PrintReads \
+        java -Xmx${task.memory.toGiga()-4}G -Djava.io.tmpdir=\$TMPDIR -jar ${params.gatk_path} -T PrintReads \
         --num_cpu_threads_per_data_thread ${task.cpus} \
         --reference_sequence ${params.genome} \
         --input_file ${bam_file} \

diff --git a/GATK/3.8-1-0-gf15c1c3ef/CatVariants.nf b/GATK/3.8-1-0-gf15c1c3ef/CatVariants.nf
@@ -14,6 +14,10 @@ process CatVariantsGVCF {
     script:
         def input_files = gvcf_files.collect{"$it"}.join(" -V ")
         """
-        java -Xmx${task.memory.toGiga()-4}G -cp ${params.gatk_path} org.broadinstitute.gatk.tools.CatVariants --reference ${params.genome} -V ${input_files} --outputFile ${sample_id}.g.vcf.gz ${params.optional}
+        java -Xmx${task.memory.toGiga()-4}G -Djava.io.tmpdir=\$TMPDIR -cp ${params.gatk_path} org.broadinstitute.gatk.tools.CatVariants \
+        --reference ${params.genome} \
+        -V ${input_files} \
+        --outputFile ${sample_id}.g.vcf.gz \
+        ${params.optional}
         """
 }
diff --git a/GATK/3.8-1-0-gf15c1c3ef/CombineVariants.nf b/GATK/3.8-1-0-gf15c1c3ef/CombineVariants.nf
@@ -14,7 +14,11 @@ process CombineVariants {
     script:
         def input_files = vcf_files.collect{"$it"}.join(" -V ")
         """
-        java -Xmx${task.memory.toGiga()-4}G -jar ${params.gatk_path} -T CombineVariants --reference_sequence ${params.genome} -V ${input_files} --out ${analysis_id}.vcf ${params.optional}
+        java -Xmx${task.memory.toGiga()-4}G -Djava.io.tmpdir=\$TMPDIR -jar ${params.gatk_path} -T CombineVariants \
+        --reference_sequence ${params.genome} \
+        -V ${input_files} \
+        --out ${analysis_id}.vcf \
+        ${params.optional}
         """
 }
 
@@ -34,6 +38,10 @@ process CombineVariantsGVCF {
     script:
         def input_files = vcf_files.collect{"$it"}.join(" -V ")
         """
-        java -Xmx${task.memory.toGiga()-4}G -jar ${params.gatk_path} -T CombineVariants --reference_sequence ${params.genome} -V ${input_files} --out ${sample_id}.g.vcf ${params.optional}
+        java -Xmx${task.memory.toGiga()-4}G -Djava.io.tmpdir=\$TMPDIR -jar ${params.gatk_path} -T CombineVariants \
+        --reference_sequence ${params.genome} \
+        -V ${input_files} \
+        --out ${sample_id}.g.vcf \
+        ${params.optional}
         """
 }
diff --git a/GATK/3.8-1-0-gf15c1c3ef/GenotypeGVCFs.nf b/GATK/3.8-1-0-gf15c1c3ef/GenotypeGVCFs.nf
@@ -14,7 +14,7 @@ process GenotypeGVCFs {
     script:
         def input_files = gvcf_files.collect{"$it"}.join(" -V ")
         """
-        java -Xmx${task.memory.toGiga()-4}G -jar ${params.gatk_path} -T GenotypeGVCFs \
+        java -Xmx${task.memory.toGiga()-4}G -Djava.io.tmpdir=\$TMPDIR -jar ${params.gatk_path} -T GenotypeGVCFs \
         --reference_sequence ${params.genome} \
         -V ${input_files} \
         --out ${analysis_id}_${interval_file.baseName}.vcf \

diff --git a/GATK/3.8-1-0-gf15c1c3ef/HaplotypeCaller.nf b/GATK/3.8-1-0-gf15c1c3ef/HaplotypeCaller.nf
@@ -14,7 +14,7 @@ process HaplotypeCaller {
     script:
         def input_files = bam_files.collect{"$it"}.join(" --input_file ")
         """
-        java -Xmx${task.memory.toGiga()-4}G -jar ${params.gatk_path} -T HaplotypeCaller \
+        java -Xmx${task.memory.toGiga()-4}G -Djava.io.tmpdir=\$TMPDIR -jar ${params.gatk_path} -T HaplotypeCaller \
         --reference_sequence ${params.genome} \
         --input_file ${input_files} \
         --intervals ${interval_file} \
@@ -38,7 +38,7 @@ process HaplotypeCallerGVCF {
 
     script:
         """
-        java -Xmx${task.memory.toGiga()-4}G -jar ${params.gatk_path} -T HaplotypeCaller \
+        java -Xmx${task.memory.toGiga()-4}G -Djava.io.tmpdir=\$TMPDIR -jar ${params.gatk_path} -T HaplotypeCaller \
         --reference_sequence ${params.genome} \
         --input_file ${bam_file} \
         --intervals ${interval_file} \

diff --git a/GATK/3.8-1-0-gf15c1c3ef/IndelRealigner.nf b/GATK/3.8-1-0-gf15c1c3ef/IndelRealigner.nf
@@ -13,7 +13,7 @@ process IndelRealigner {
 
     script:
         """
-        java -Xmx${task.memory.toGiga()-4}G -jar ${params.gatk_path} -T IndelRealigner \
+        java -Xmx${task.memory.toGiga()-4}G -Djava.io.tmpdir=\$TMPDIR -jar ${params.gatk_path} -T IndelRealigner \
         --reference_sequence ${params.genome} \
         --input_file ${bam_file} \
         --intervals ${chr} \

diff --git a/GATK/3.8-1-0-gf15c1c3ef/RealignerTargetCreator.nf b/GATK/3.8-1-0-gf15c1c3ef/RealignerTargetCreator.nf
@@ -13,7 +13,7 @@ process RealignerTargetCreator {
 
     script:
         """
-        java -Xmx${task.memory.toGiga()-4}G -jar $params.gatk_path -T RealignerTargetCreator \
+        java -Xmx${task.memory.toGiga()-4}G -Djava.io.tmpdir=\$TMPDIR -jar $params.gatk_path -T RealignerTargetCreator \
         --reference_sequence ${params.genome} \
         --input_file ${bam_file} \
         --intervals ${chr} \

diff --git a/GATK/3.8-1-0-gf15c1c3ef/SelectVariants.nf b/GATK/3.8-1-0-gf15c1c3ef/SelectVariants.nf
@@ -13,6 +13,10 @@ process SelectVariantsSample {
 
     script:
         """
-        java -Xmx${task.memory.toGiga()-4}G -jar ${params.gatk_path} -T SelectVariants --reference_sequence ${params.genome} -V ${vcf_file} --out ${sample_id}_${vcf_file.baseName}.vcf -sn ${sample_id}
+        java -Xmx${task.memory.toGiga()-4}G -Djava.io.tmpdir=\$TMPDIR -jar ${params.gatk_path} -T SelectVariants \
+        --reference_sequence ${params.genome} \
+        -V ${vcf_file} \
+        --out ${sample_id}_${vcf_file.baseName}.vcf \
+        -sn ${sample_id}
         """
 }
diff --git a/GATK/3.8-1-0-gf15c1c3ef/UnifiedGenotyper.nf b/GATK/3.8-1-0-gf15c1c3ef/UnifiedGenotyper.nf
@@ -14,6 +14,10 @@ process UnifiedGenotyper {
     script:
 
         """
-        java -Xmx${task.memory.toGiga()-4}G -jar ${params.gatk_path} -T UnifiedGenotyper --reference_sequence ${params.genome} --input_file ${bam_file} --out ${sample_id}.vcf ${params.optional}
+        java -Xmx${task.memory.toGiga()-4}G -Djava.io.tmpdir=\$TMPDIR -jar ${params.gatk_path} -T UnifiedGenotyper \
+        --reference_sequence ${params.genome} \
+        --input_file ${bam_file} \
+        --out ${sample_id}.vcf \
+        ${params.optional}
         """
 }
diff --git a/GATK/3.8-1-0-gf15c1c3ef/VariantFiltration.nf b/GATK/3.8-1-0-gf15c1c3ef/VariantFiltration.nf
@@ -13,12 +13,22 @@ process VariantFiltrationSnpIndel {
 
     script:
         """
-        java -Xmx${task.memory.toGiga()-4}G -jar ${params.gatk_path} -T SelectVariants --reference_sequence ${params.genome} -V $vcf_file --out ${vcf_file.baseName}.snp.vcf --selectTypeToExclude INDEL
-        java -Xmx${task.memory.toGiga()-4}G -jar ${params.gatk_path} -T SelectVariants --reference_sequence ${params.genome} -V $vcf_file --out ${vcf_file.baseName}.indel.vcf --selectTypeToInclude INDEL
+        java -Xmx${task.memory.toGiga()-4}G -Djava.io.tmpdir=\$TMPDIR -jar ${params.gatk_path} -T SelectVariants \
+        --reference_sequence ${params.genome} -V $vcf_file --out ${vcf_file.baseName}.snp.vcf --selectTypeToExclude INDEL
 
-        java -Xmx${task.memory.toGiga()-4}G -jar ${params.gatk_path} -T VariantFiltration --reference_sequence ${params.genome} -V ${vcf_file.baseName}.snp.vcf --out ${vcf_file.baseName}.snp_filter.vcf ${params.snp_filter} ${params.snp_cluster}
-        java -Xmx${task.memory.toGiga()-4}G -jar ${params.gatk_path} -T VariantFiltration --reference_sequence ${params.genome} -V ${vcf_file.baseName}.indel.vcf --out ${vcf_file.baseName}.indel_filter.vcf ${params.indel_filter}
+        java -Xmx${task.memory.toGiga()-4}G -Djava.io.tmpdir=\$TMPDIR -jar ${params.gatk_path} -T SelectVariants \
+        --reference_sequence ${params.genome} -V $vcf_file --out ${vcf_file.baseName}.indel.vcf --selectTypeToInclude INDEL
 
-        java -Xmx${task.memory.toGiga()-4}G -jar ${params.gatk_path} -T CombineVariants --reference_sequence ${params.genome} -V ${vcf_file.baseName}.snp_filter.vcf -V ${vcf_file.baseName}.indel_filter.vcf --out ${vcf_file.baseName}.filter.vcf --assumeIdenticalSamples
+        java -Xmx${task.memory.toGiga()-4}G -Djava.io.tmpdir=\$TMPDIR -jar ${params.gatk_path} -T VariantFiltration \
+        --reference_sequence ${params.genome} -V ${vcf_file.baseName}.snp.vcf --out ${vcf_file.baseName}.snp_filter.vcf \
+        ${params.snp_filter} ${params.snp_cluster}
+        
+        java -Xmx${task.memory.toGiga()-4}G -Djava.io.tmpdir=\$TMPDIR -jar ${params.gatk_path} -T VariantFiltration \
+        --reference_sequence ${params.genome} -V ${vcf_file.baseName}.indel.vcf --out ${vcf_file.baseName}.indel_filter.vcf \
+        ${params.indel_filter}
+
+        java -Xmx${task.memory.toGiga()-4}G -Djava.io.tmpdir=\$TMPDIR -jar ${params.gatk_path} -T CombineVariants \
+        --reference_sequence ${params.genome} -V ${vcf_file.baseName}.snp_filter.vcf -V ${vcf_file.baseName}.indel_filter.vcf \
+        --out ${vcf_file.baseName}.filter.vcf --assumeIdenticalSamples
         """
 }
diff --git a/GATK/4.1.3.0/BaseRecalibration.nf b/GATK/4.1.3.0/BaseRecalibration.nf
@@ -1,5 +1,3 @@
-
-
 process BaseRecalibration {
     tag {"GATK BaseRecalibration ${sample_id}.${int_tag}"}
     label 'GATK_4_1_3_0'
@@ -16,13 +14,14 @@ process BaseRecalibration {
     script:
         int_tag = interval_file.toRealPath().toString().split("/")[-2]
         """
-        gatk --java-options "-Xmx${task.memory.toGiga()-4}g -Djava.io.tmpdir=\$TMPDIR"\
+        gatk --java-options "-Xmx${task.memory.toGiga()-4}g -Djava.io.tmpdir=\$TMPDIR" \
         ApplyBQSR \
         --input $bam \
         --output ${sample_id}.${int_tag}_recalibrated.bam \
         -R ${params.genome_fasta} \
         --create-output-bam-index true \
         --bqsr-recal-file ${recal_table} \
-        -L $interval_file
+        -L $interval_file \
+        --tmp-dir \$TMPDIR
         """
 }
diff --git a/GATK/4.1.3.0/BaseRecalibrationTable.nf b/GATK/4.1.3.0/BaseRecalibrationTable.nf
@@ -1,4 +1,3 @@
-
 process BaseRecalibrationTable {
     tag {"GATK BaseRecalibrationTable ${sample_id}.${int_tag}"}
     label 'GATK_4_1_3_0'
@@ -23,7 +22,8 @@ process BaseRecalibrationTable {
         --output ${sample_id}.${int_tag}.recal.table \
         -R ${params.genome_fasta} \
         $known \
-        -L $interval_file
+        -L $interval_file \
+        --tmp-dir \$TMPDIR
         """
 }
 
diff --git a/GATK/4.1.3.0/CollectMultipleMetrics.nf b/GATK/4.1.3.0/CollectMultipleMetrics.nf
@@ -1,4 +1,3 @@
-
 process CollectMultipleMetrics {
   tag {"GATK CollectMultipleMetrics ${sample_id}"}
   label 'GATK_4_1_3_0'
@@ -19,6 +18,7 @@ process CollectMultipleMetrics {
     -I $bam \
     -O ${sample_id}.multiple_metrics\
     -R ${params.genome_fasta} \
+    --TMP_DIR \$TMPDIR \
     ${params.optional}
     """
 }
diff --git a/GATK/4.1.3.0/CollectWGSMetrics.nf b/GATK/4.1.3.0/CollectWGSMetrics.nf
@@ -1,4 +1,3 @@
-
 process CollectWGSMetrics {
   tag {"GATK CollectWGSMetrics ${sample_id}"}
   label 'GATK_4_1_3_0'
@@ -19,6 +18,7 @@ process CollectWGSMetrics {
     -I $bam \
     -O ${sample_id}.wgs_metrics.txt \
     -R ${params.genome_fasta} \
+    --TMP_DIR \$TMPDIR \
     ${params.optional}
     sed -i 's/picard\\.analysis\\.WgsMetrics/picard\\.analysis\\.CollectWgsMetrics\\\$WgsMetrics/' ${sample_id}.wgs_metrics.txt
     """

diff --git a/GATK/4.1.3.0/CombineGVCFs.nf b/GATK/4.1.3.0/CombineGVCFs.nf
@@ -19,6 +19,7 @@ process CombineGVCFs {
         -R ${params.genome_fasta} \
         -V $vcfs \
         -O ${run_id}.${interval}.g.vcf \
-        -L $interval_file
+        -L $interval_file \
+        --tmp-dir \$TMPDIR
         """
 }
diff --git a/GATK/4.1.3.0/GatherBaseRecalibrationTables.nf b/GATK/4.1.3.0/GatherBaseRecalibrationTables.nf
@@ -1,4 +1,3 @@
-
 process GatherBaseRecalibrationTables {
     tag {"GATK GatherBaseRecalibrationTables ${sample_id}"}
     label 'GATK_4_1_3_0'
@@ -19,5 +18,6 @@ process GatherBaseRecalibrationTables {
         GatherBQSRReports \
         -I $tables \
         --output ${sample_id}.recal.table \
+        --tmp-dir \$TMPDIR
         """
 }
diff --git a/GATK/4.1.3.0/GenotypeGVCFs.nf b/GATK/4.1.3.0/GenotypeGVCFs.nf
@@ -19,6 +19,7 @@ process GenotypeGVCFs {
         -O ${run_id}.${interval}.vcf \
         -R ${params.genome_fasta} \
         -D ${params.genome_dbsnp} \
-        -L $interval_file
+        -L $interval_file \
+        --tmp-dir \$TMPDIR
         """
 }
diff --git a/GATK/4.1.3.0/HaplotypeCaller.nf b/GATK/4.1.3.0/HaplotypeCaller.nf
@@ -21,6 +21,7 @@ process HaplotypeCaller {
         -I $bam \
         --output ${sample_id}.${int_tag}${ext} \
         -R $params.genome_fasta \
-        -L $interval_file
+        -L $interval_file \
+        --tmp-dir \$TMPDIR
         """
 }
diff --git a/GATK/4.1.3.0/MergeVCFs.nf b/GATK/4.1.3.0/MergeVCFs.nf
@@ -17,10 +17,11 @@ process MergeVCFs {
         vcfs = vcf_chunks.join(' -INPUT ')
 
         """
-        gatk --java-options "-Xmx${task.memory.toGiga()-4}g -Djava.io.tmpdir=\$PWD" \
+        gatk --java-options "-Xmx${task.memory.toGiga()-4}g -Djava.io.tmpdir=\$TMPDIR" \
         SortVcf \
         --INPUT $vcfs \
-        --OUTPUT ${id}${ext}
+        --OUTPUT ${id}${ext} \
+        --TMP_DIR \$TMPDIR
 
         bgzip ${id}${ext}
         tabix ${id}${ext}.gz

diff --git a/GATK/4.1.3.0/SamToFastq.nf b/GATK/4.1.3.0/SamToFastq.nf
@@ -1,4 +1,3 @@
-
 process SamToFastq {
     tag {"GATK SamToFastq ${sample_id} "}
     label 'GATK_4_1_3_0'
@@ -23,5 +22,6 @@ process SamToFastq {
         --FASTQ ${sample_id}_${flowcell}_R1_001.fastq.gz \
         --SECOND_END_FASTQ ${sample_id}_${flowcell}_R2_001.fastq.gz \
         --INCLUDE_NON_PF_READS true \
+        --TMP_DIR \$TMPDIR
         """
 }
diff --git a/GATK/4.1.3.0/SelectVariants.nf b/GATK/4.1.3.0/SelectVariants.nf
@@ -19,6 +19,7 @@ process SelectVariants {
         -R ${params.genome_fasta} \
         -V $vcf \
         -O ${run_id}.${interval}.${type}.tmp.vcf \
-        $select_type
+        $select_type \
+        --tmp-dir \$TMPDIR
         """
 }
diff --git a/GATK/4.1.3.0/SplitIntervals.nf b/GATK/4.1.3.0/SplitIntervals.nf
@@ -17,9 +17,10 @@ process SplitIntervals {
         """
         gatk --java-options "-Xmx${task.memory.toGiga()-4}g -Djava.io.tmpdir=\${TMPDIR}" \
         IntervalListTools \
-            -I ${scatter_interval_list} \
-            ${params.optional} \
-            --BREAK_BANDS_AT_MULTIPLES_OF $break_bands_at_multiples_of \
-            -O .
+        -I ${scatter_interval_list} \
+        ${params.optional} \
+        --BREAK_BANDS_AT_MULTIPLES_OF $break_bands_at_multiples_of \
+        -O . \
+        --TMP_DIR \$TMPDIR
         """
 }
diff --git a/GATK/4.1.3.0/SplitNCigarReads.nf b/GATK/4.1.3.0/SplitNCigarReads.nf
@@ -13,8 +13,9 @@ process SplitNCigarReads {
 
     script:
         """
-        gatk --java-options "-Xmx${task.memory.toGiga()-4}g" \
-        SplitNCigarReads --tmp-dir \$PWD \
+        gatk --java-options "-Xmx${task.memory.toGiga()-4}g -Djava.io.tmpdir=\$TMPDIR" \
+        SplitNCigarReads \
+        --tmp-dir \$TMPDIR \
         -R ${params.genome_fasta} \
         -I ${bam_file} \
         --refactor-cigar-string \

diff --git a/GATK/4.1.3.0/VariantAnnotator.nf b/GATK/4.1.3.0/VariantAnnotator.nf
@@ -1,4 +1,3 @@
-
 process VariantAnnotator {
     tag {"GATK VariantAnnotator ${run_id}"}
     label 'GATK_4_1_3_0'
@@ -23,5 +22,6 @@ process VariantAnnotator {
         -V $vcf \
         --output ${vcf.baseName}_${db_name}.vcf \
         --dbsnp ${params.genome_variant_annotator_db} \
+        --tmp-dir \$TMPDIR
         """
 }
diff --git a/GATK/4.1.3.0/VariantFiltration.nf b/GATK/4.1.3.0/VariantFiltration.nf
@@ -1,4 +1,3 @@
-
 process VariantFiltration {
     tag {"GATK VariantFiltration ${run_id}.${interval}.${type}"}
     label 'GATK_4_1_3_0'
@@ -27,6 +26,7 @@ process VariantFiltration {
         -R $params.genome_fasta \
         -V $vcf \
         -O ${run_id}.${interval}.${type}.filtered_variants.vcf \
+        --tmp-dir \$TMPDIR \
         $filter_criteria
         """
 }
diff --git a/GATK/4.2.1.0/GenotypeGvcfs.nf b/GATK/4.2.1.0/GenotypeGvcfs.nf
@@ -21,11 +21,12 @@ process GenotypeGVCFs {
         ext_vcf = params.compress || gvcf_files.getExtension() == ".gz" ? ".vcf.gz" : ".vcf"
         ext_vcf_index = params.compress || gvcf_files.getExtension() == ".gz" ? ".tbi" : ".idx"
         """
-        gatk --java-options "-Xmx${task.memory.toGiga()-4}G" GenotypeGVCFs \
+        gatk --java-options "-Xmx${task.memory.toGiga()-4}G -Djava.io.tmpdir=\$TMPDIR" GenotypeGVCFs \
         --reference ${params.genome} \
         --variant $input_files \
         --output ${analysis_id}_${interval_file.simpleName}${ext_vcf} \
         --intervals ${interval_file} \
+        --tmp-dir \$TMPDIR \
         ${params.optional}
         """
 }
@@ -53,11 +54,12 @@ process GenotypeGVCF {
         ext_vcf = params.compress || gvcf_files.getExtension() == ".gz" ? ".vcf.gz" : ".vcf"
         ext_vcf_index = params.compress || gvcf_files.getExtension() == ".gz" ? ".tbi" : ".idx"
         """
-        gatk --java-options "-Xmx${task.memory.toGiga()-4}G" GenotypeGVCFs \
+        gatk --java-options "-Xmx${task.memory.toGiga()-4}G -Djava.io.tmpdir=\$TMPDIR" GenotypeGVCFs \
         --reference ${params.genome} \
         --variant $input_files \
         --output ${sample_id}_${interval_file.simpleName}${ext_vcf} \
         --intervals ${interval_file} \
+        --tmp-dir \$TMPDIR \
         ${params.optional}
         """
 }
diff --git a/GATK/4.2.1.0/HaplotypeCaller.nf b/GATK/4.2.1.0/HaplotypeCaller.nf
@@ -21,11 +21,12 @@ process HaplotypeCaller {
         ext_vcf = params.compress ? ".vcf.gz" : ".vcf"
         ext_vcf_index = params.compress ? ".tbi" : ".idx"
         """
-        gatk --java-options "-Xmx${task.memory.toGiga()-4}G" HaplotypeCaller \
+        gatk --java-options "-Xmx${task.memory.toGiga()-4}G -Djava.io.tmpdir=\$TMPDIR" HaplotypeCaller \
         --reference ${params.genome} \
         --input ${input_files} \
         --intervals ${interval_file} \
         --output ${analysis_id}.${interval_file.simpleName}${ext_vcf} \
+        --tmp-dir \$TMPDIR \
         ${params.optional}
         """
 }
@@ -54,12 +55,13 @@ process HaplotypeCallerGVCF {
         ext_gvcf = params.compress ? ".g.vcf.gz" : ".g.vcf"
         ext_gvcf_index = params.compress ? ".tbi" : ".idx"
         """
-        gatk --java-options "-Xmx${task.memory.toGiga()-4}G" HaplotypeCaller \
+        gatk --java-options "-Xmx${task.memory.toGiga()-4}G -Djava.io.tmpdir=\$TMPDIR" HaplotypeCaller \
         --reference ${params.genome} \
         --input ${bam_file} \
         --intervals ${interval_file} \
         --output ${sample_id}_${interval_file.simpleName}${ext_gvcf} \
         --emit-ref-confidence ${params.emit_ref_confidence} \
+        --tmp-dir \$TMPDIR \
         ${params.optional}
         """
 }