diff --git a/main.nf b/main.nf index 23b6e246ac..866221bdfa 100644 --- a/main.nf +++ b/main.nf @@ -352,7 +352,7 @@ process CreateRecalibrationTable { BaseRecalibrator \ --input ${bam} \ --output ${idSample}.recal.table \ - --TMP_DIR /tmp \ + --tmp-dir /tmp \ -R ${genomeFile} \ -L ${intervals} \ --known-sites ${dbsnp} \ @@ -418,8 +418,8 @@ process RecalibrateBam { --input ${bam} \ --output ${idSample}.recal.bam \ -L ${intervals} \ - --create-output-bam-index true \ - --bqsr-recal-file ${recalibrationReport} + --create-output-bam-index true \ + --bqsr-recal-file ${recalibrationReport} """ } // Creating a TSV file to restart from this step