diff --git a/conf/modules/align_bwa_bwamem2.config b/conf/modules/align_bwa_bwamem2.config
index f0725de9..30d14cf4 100644
--- a/conf/modules/align_bwa_bwamem2.config
+++ b/conf/modules/align_bwa_bwamem2.config
@@ -19,12 +19,14 @@ process {
 
     withName: '.*ALIGN:ALIGN_BWA_BWAMEM2:BWAMEM2_MEM' {
         ext.args = { "-M -K 100000000 -R ${meta.read_group}" }
+        ext.args2 = { "-T ./samtools_sort_tmp" }
         ext.prefix = { "${meta.id}_sorted" }
         ext.when = { params.aligner.equals("bwamem2") }
     }
 
     withName: '.*ALIGN:ALIGN_BWA_BWAMEM2:BWA_MEM' {
         ext.args = { "-M -K 100000000 -R ${meta.read_group}" }
+        ext.args2 = { "-T ./samtools_sort_tmp" }
         ext.prefix = { "${meta.id}_sorted" }
         ext.when = { params.aligner.equals("bwa") }
     }
diff --git a/conf/modules/prepare_references.config b/conf/modules/prepare_references.config
index 04416bcd..5d24cefa 100644
--- a/conf/modules/prepare_references.config
+++ b/conf/modules/prepare_references.config
@@ -115,7 +115,12 @@ process {
     }
 
     withName: '.*PREPARE_REFERENCES:GATK_PREPROCESS_WGS' {
-        ext.args =  { "--padding 0 --interval-merging-rule OVERLAPPING_ONLY --exclude-intervals ${params.mito_name}" }
+        ext.args =  { [
+            '--padding 0',
+            '--interval-merging-rule OVERLAPPING_ONLY',
+            "--exclude-intervals ${params.mito_name}",
+            "--temp-dir ./"
+            ].join(' ') }
         ext.when = { params.analysis_type.equals("wgs") && !params.readcount_intervals }
     }
 
diff --git a/conf/modules/rank_variants.config b/conf/modules/rank_variants.config
index 3d8f1804..cd5ab7c9 100644
--- a/conf/modules/rank_variants.config
+++ b/conf/modules/rank_variants.config
@@ -21,22 +21,24 @@ process {
         ext.prefix = { "${meta.id}_sv_genmod_annotate_${meta.set}" }
         ext.args = { [
             '--annotate_regions',
-            params.genome.equals('GRCh37') ? '--genome-build 37' : '--genome-build 38'
+            params.genome.equals('GRCh37') ? '--genome-build 37' : '--genome-build 38',
+            '--temp_dir ./'
             ].join(' ') }
     }
 
     withName: '.*RANK_VARIANTS_SV:GENMOD_MODELS' {
         ext.prefix = { "${meta.id}_sv_genmod_models_${meta.set}" }
-        ext.args = " --whole_gene "
+        ext.args = "--whole_gene --temp_dir ./"
     }
 
     withName: '.*RANK_VARIANTS_SV:GENMOD_SCORE' {
         ext.prefix = { "${meta.id}_sv_genmod_score_${meta.set}" }
-        ext.args = " --rank_results "
+        ext.args = "--rank_results"
     }
 
     withName: '.*RANK_VARIANTS_SV:GENMOD_COMPOUND' {
         ext.prefix = { "${meta.id}_sv_genmod_compound_${meta.set}" }
+        ext.args = "--temp_dir ./"
     }
 
     withName: '.*RANK_VARIANTS_SV:BCFTOOLS_SORT' {
@@ -72,22 +74,24 @@ process {
         ext.prefix = { "${meta.id}_snv_genmod_annotate_${meta.set}" }
         ext.args = { [
             '--annotate_regions',
-            params.genome.equals('GRCh37') ? '--genome-build 37' : '--genome-build 38'
+            params.genome.equals('GRCh37') ? '--genome-build 37' : '--genome-build 38',
+            '--temp_dir ./'
             ].join(' ') }
     }
 
     withName: '.*RANK_VARIANTS_SNV:GENMOD_MODELS' {
         ext.prefix = { "${meta.id}_snv_genmod_models_${meta.set}" }
-        ext.args = " --whole_gene "
+        ext.args = "--whole_gene --temp_dir ./"
     }
 
     withName: '.*RANK_VARIANTS_SNV:GENMOD_SCORE' {
         ext.prefix = { "${meta.id}_snv_genmod_score_${meta.set}" }
-        ext.args = " --rank_results "
+        ext.args = "--rank_results"
     }
 
     withName: '.*RANK_VARIANTS_SNV:GENMOD_COMPOUND' {
         ext.prefix = { "${meta.id}_snv_genmod_compound_${meta.set}" }
+        ext.args = "--temp_dir ./"
     }
 
     withName: '.*RANK_VARIANTS_SNV:BCFTOOLS_SORT' {
@@ -122,22 +126,24 @@ process {
         ext.prefix = { "${meta.id}_mt_genmod_annotate_${meta.set}" }
         ext.args = { [
             '--annotate_regions',
-            params.genome.equals('GRCh37') ? '--genome-build 37' : '--genome-build 38'
+            params.genome.equals('GRCh37') ? '--genome-build 37' : '--genome-build 38',
+            '--temp_dir ./'
             ].join(' ') }
     }
 
     withName: '.*RANK_VARIANTS_MT:GENMOD_MODELS' {
         ext.prefix = { "${meta.id}_mt_genmod_models_${meta.set}" }
-        ext.args = " --whole_gene "
+        ext.args = "--whole_gene --temp_dir ./"
     }
 
     withName: '.*RANK_VARIANTS_MT:GENMOD_SCORE' {
         ext.prefix = { "${meta.id}_mt_genmod_score_${meta.set}" }
-        ext.args = " --rank_results "
+        ext.args = "--rank_results"
     }
 
     withName: '.*RANK_VARIANTS_MT:GENMOD_COMPOUND' {
         ext.prefix = { "${meta.id}_mt_genmod_compound_${meta.set}" }
+        ext.args = "--temp_dir ./"
     }
 
     withName: '.*RANK_VARIANTS_MT:BCFTOOLS_SORT' {
diff --git a/conf/modules/raredisease.config b/conf/modules/raredisease.config
index a4f1bbac..12ff0f37 100644
--- a/conf/modules/raredisease.config
+++ b/conf/modules/raredisease.config
@@ -33,7 +33,7 @@ process {
 process {
 
     withName: '.*RAREDISEASE:FASTQC' {
-        ext.args = '--quiet'
+        ext.args = '--quiet --dir ./'
         publishDir = [
             path: { "${params.outdir}/fastqc/${meta.id}" },
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename },