diff --git a/modules/local/mutect2.nf b/modules/local/mutect2.nf index c5964a9..87ec0f3 100644 --- a/modules/local/mutect2.nf +++ b/modules/local/mutect2.nf @@ -20,6 +20,7 @@ process MUTECT2 { -callable-depth 6 \ --native-pair-hmm-threads ${task.cpus} \ --max-reads-per-alignment-start 0 \ + --tmp-dir \$PWD \ -I ${bam_file} \ -O raw.vcf.gz @@ -27,6 +28,7 @@ process MUTECT2 { -R ${reference} \ --min-reads-per-strand 2 \ -V raw.vcf.gz \ + --tmp-dir \$PWD \ -O ${bam_file.baseName}.vcf.gz bcftools norm \