diff --git a/modules/01_prepare_bam.nf b/modules/01_prepare_bam.nf index f134357..f9a9734 100644 --- a/modules/01_prepare_bam.nf +++ b/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 ${bam} """ } diff --git a/modules/02_mark_duplicates.nf b/modules/02_mark_duplicates.nf index 9ff86ea..7395a00 100644 --- a/modules/02_mark_duplicates.nf +++ b/modules/02_mark_duplicates.nf @@ -32,7 +32,7 @@ process MARK_DUPLICATES { --SORT_ORDER coordinate gatk MarkDuplicates \ - --java-options '-Xmx${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 \ diff --git a/modules/03_metrics.nf b/modules/03_metrics.nf index 43909fa..0dfeecb 100644 --- a/modules/03_metrics.nf +++ b/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 ${params.reference} \ diff --git a/modules/04_realignment_around_indels.nf b/modules/04_realignment_around_indels.nf index 1f86288..bcba6cc 100644 --- a/modules/04_realignment_around_indels.nf +++ b/modules/04_realignment_around_indels.nf @@ -31,12 +31,12 @@ process REALIGNMENT_AROUND_INDELS { """ mkdir tmp - gatk3 -Xmx${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 ${params.reference} \ diff --git a/modules/05_bqsr.nf b/modules/05_bqsr.nf index c893929..df0f228 100644 --- a/modules/05_bqsr.nf +++ b/modules/05_bqsr.nf @@ -26,14 +26,14 @@ process BQSR { mkdir tmp gatk BaseRecalibrator \ - --java-options '-Xmx${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} \ diff --git a/nextflow.config b/nextflow.config index 8cf89d7..d899e71 100644 --- a/nextflow.config +++ b/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 {