diff --git a/src/nf_modules/star/main_2.7.8a.nf b/src/nf_modules/star/main_2.7.8a.nf index d865c751fe9e576e4aa023a79f6363edb276e8a4..389a2eef50edbcbacb2b7d691b17cd815d6d999c 100644 --- a/src/nf_modules/star/main_2.7.8a.nf +++ b/src/nf_modules/star/main_2.7.8a.nf @@ -34,6 +34,7 @@ process index_with_gtf { tuple val(genome_id), path ("*"), emit: index script: + memory = "${task.memory}" - ~/\s*GB/ """ STAR --runThreadN ${task.cpus} --runMode genomeGenerate \ --genomeDir ./ \ @@ -250,6 +251,7 @@ process mapping2fusion { tuple val(reads_id), path("*.bam"), emit: bam script: + memory = "${task.memory}" - ~/\s*GB/ if (reads_id instanceof List){ file_prefix = reads_id[0] } else { @@ -281,7 +283,8 @@ STAR --runThreadN ${task.cpus} \ --chimScoreJunctionNonGTAG 0 \ --chimScoreSeparation 1 \ --chimSegmentReadGapMax 3 \ ---chimMultimapNmax 50 +--chimMultimapNmax 50 \ +--limitBAMsortRAM ${memory}000000000 mv ${reads_id}.Aligned.sortedByCoord.out.bam ${reads_id}.bam """ @@ -311,7 +314,8 @@ STAR --runThreadN ${task.cpus} \ --chimScoreJunctionNonGTAG 0 \ --chimScoreSeparation 1 \ --chimSegmentReadGapMax 3 \ ---chimMultimapNmax 50 +--chimMultimapNmax 50 \ +--limitBAMsortRAM ${memory}000000000 mv ${reads_id}.Aligned.sortedByCoord.out.bam ${reads_id}.bam """