Merge pull request #6 from TRON-Bioinformatics/fix-tmp-folder-issue

ensure local temp folder is used

Author: priesgo

modules/01_prepare_bam.nf

@@ -31,7 +31,7 @@ process PREPARE_BAM {
     mkdir tmp
 
     gatk AddOrReplaceReadGroups \
-    --java-options '-Xmx${params.prepare_bam_memory} -Djava.io.tmpdir=tmp' \
+    --java-options '-Xmx${params.prepare_bam_memory} -Djava.io.tmpdir=./tmp' \
     --VALIDATION_STRINGENCY SILENT \
     --INPUT ${bam} \
     --OUTPUT /dev/stdout \
@@ -42,11 +42,11 @@ process PREPARE_BAM {
     --RGLB 1 \
     --RGPL ${params.platform} ${order} | \
     gatk CleanSam \
-    --java-options '-Xmx${params.prepare_bam_memory} -Djava.io.tmpdir=tmp' \
+    --java-options '-Xmx${params.prepare_bam_memory} -Djava.io.tmpdir=./tmp' \
     --INPUT /dev/stdin \
     --OUTPUT /dev/stdout | \
     gatk ReorderSam \
-    --java-options '-Xmx${params.prepare_bam_memory} -Djava.io.tmpdir=tmp' \
+    --java-options '-Xmx${params.prepare_bam_memory} -Djava.io.tmpdir=./tmp' \
     --INPUT /dev/stdin \
     --OUTPUT ${name}.prepared.bam \
     --SEQUENCE_DICTIONARY ${params.reference}
@@ -71,7 +71,7 @@ process INDEX_BAM {
     mkdir tmp
 
     gatk BuildBamIndex \
-    --java-options '-Xmx8g  -Djava.io.tmpdir=tmp' \
+    --java-options '-Xmx8g  -Djava.io.tmpdir=./tmp' \
     --INPUT  ${bam}
     """
 }

modules/02_mark_duplicates.nf

@@ -32,7 +32,7 @@ process MARK_DUPLICATES {
     --SORT_ORDER coordinate
 
     gatk MarkDuplicates \
-    --java-options '-Xmx${params.mark_duplicates_memory}  -Djava.io.tmpdir=tmp' \
+    --java-options '-Xmx${params.mark_duplicates_memory}  -Djava.io.tmpdir=./tmp' \
     --INPUT  ${name}.sorted.bam \
     --OUTPUT ${name}.dedup.bam \
     --ASSUME_SORT_ORDER coordinate \

modules/03_metrics.nf

@@ -37,7 +37,7 @@ process HS_METRICS {
     --SEQUENCE_DICTIONARY ${bam}
 
     gatk CollectHsMetrics \
-    --java-options '-Xmx${params.metrics_memory}  -Djava.io.tmpdir=tmp' \
+    --java-options '-Xmx${params.metrics_memory}  -Djava.io.tmpdir=./tmp' \
     --INPUT  ${bam} \
     --OUTPUT ${name}.hs_metrics.txt \
     --TARGET_INTERVALS my.intervals \
@@ -66,7 +66,7 @@ process METRICS {
     mkdir tmp
 
     gatk CollectMultipleMetrics \
-    --java-options '-Xmx${params.metrics_memory}  -Djava.io.tmpdir=tmp' \
+    --java-options '-Xmx${params.metrics_memory}  -Djava.io.tmpdir=./tmp' \
     --INPUT  ${bam} \
     --OUTPUT ${name} \
     --REFERENCE_SEQUENCE ${params.reference} \

modules/04_realignment_around_indels.nf

@@ -31,12 +31,12 @@ process REALIGNMENT_AROUND_INDELS {
     """
     mkdir tmp
 
-    gatk3 -Xmx${params.realignment_around_indels_memory} -Djava.io.tmpdir=tmp -T RealignerTargetCreator \
+    gatk3 -Xmx${params.realignment_around_indels_memory} -Djava.io.tmpdir=./tmp -T RealignerTargetCreator \
     --input_file ${bam} \
     --out ${name}.RA.intervals \
     --reference_sequence ${params.reference} ${known_indels1} ${known_indels2}
 
-    gatk3 -Xmx${params.realignment_around_indels_memory} -Djava.io.tmpdir=tmp -T IndelRealigner \
+    gatk3 -Xmx${params.realignment_around_indels_memory} -Djava.io.tmpdir=./tmp -T IndelRealigner \
     --input_file ${bam} \
     --out ${name}.realigned.bam \
     --reference_sequence ${params.reference} \

modules/05_bqsr.nf

@@ -26,14 +26,14 @@ process BQSR {
     mkdir tmp
 
     gatk BaseRecalibrator \
-    --java-options '-Xmx${params.bqsr_memory} -Djava.io.tmpdir=tmp' \
+    --java-options '-Xmx${params.bqsr_memory} -Djava.io.tmpdir=./tmp' \
     --input ${bam} \
     --output ${name}.recalibration_report.grp \
     --reference ${params.reference} \
     --known-sites ${params.dbsnp}
 
     gatk ApplyBQSR \
-    --java-options '-Xmx${params.bqsr_memory} -Djava.io.tmpdir=tmp' \
+    --java-options '-Xmx${params.bqsr_memory} -Djava.io.tmpdir=./tmp' \
     --input ${bam} \
     --output ${name}.preprocessed.bam \
     --reference ${params.reference} \

nextflow.config

@@ -46,7 +46,7 @@ process.shell = ['/bin/bash', '-euo', 'pipefail']
 
 cleanup = true
 
-VERSION = '1.8.0'
+VERSION = '1.8.1'
 DOI = 'https://zenodo.org/badge/latestdoi/358400957'
 
 manifest {