Merge pull request #668 from nvnieuwk/add/limitBamSortRam

add `--limit_bam_sort_ram`

Author: nvnieuwk

CHANGELOG.md

@@ -42,6 +42,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Added the `seq_platform` and `seq_center` fields to the samplesheet. These values can be used to overwrite the value of `--seq_platform` and `--seq_center` on a sample-by-sample basis [#654](https://github.com/nf-core/rnafusion/pull/654)
 - Moved strandedness determination for picard collectrnaseqmetrics into modules.config [#658](https://github.com/nf-core/rnafusion/pull/658)
 - Using option `--human_gencode_filter` while building STARFusion references for human species [#657](https://github.com/nf-core/rnafusion/pull/657)
+- Added `--star_limit_bam_sort_ram` to set the maximum memory for sorting the BAM files in STAR. [#668](https://github.com/nf-core/rnafusion/pull/668)
 - Update STAR-Fusion to 1.15.0 and update nf-core modules [#664](https://github.com/nf-core/rnafusion/pull/664)
 - Update fusionreport 4.0.0 that replaces the score of a fusion with a Fusion Indication Index [#667](https://github.com/nf-core/rnafusion/pull/667)
 

conf/modules.config

@@ -253,27 +253,30 @@ process {
             mode: params.publish_dir_mode,
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
         ]
-        ext.args = { "--outReadsUnmapped None  \
-            --outSAMattrRGline 'ID:${meta.id}' 'SM:${meta.id}'${meta.seq_center ? " 'CN:${meta.seq_center}'": ''}${meta.seq_platform ? "' PL:${meta.seq_platform}'": ''} \
-            --outSAMstrandField intronMotif \
-            --chimOutJunctionFormat 1 \
-            --twopassMode None \
-            --outFilterMultimapNmax 50 \
-            --chimMultimapNmax 50 \
-            --quantMode GeneCounts \
-            --outSAMunmapped Within \
-            --readFilesCommand zcat  \
-            --alignSJstitchMismatchNmax 5 -1 5 5 \
-            --outSAMtype BAM SortedByCoordinate \
-            --chimSegmentMin 10 \
-            --peOverlapNbasesMin 10 \
-            --alignSplicedMateMapLminOverLmate 0.5 \
-            --chimJunctionOverhangMin 10 \
-            --chimScoreJunctionNonGTAG 0 \
-            --chimScoreDropMax 30 \
-            --chimScoreSeparation 1  \
-            --chimSegmentReadGapMax 3 \
-            --chimOutType Junctions WithinBAM" }
+        ext.args = { [
+            "--outReadsUnmapped None",
+            "--outSAMattrRGline 'ID:${meta.id}' 'SM:${meta.id}'${meta.seq_center ? " 'CN:${meta.seq_center}'": ''}${meta.seq_platform ? "' PL:${meta.seq_platform}'": ''}",
+            "--outSAMstrandField intronMotif",
+            "--chimOutJunctionFormat 1",
+            "--twopassMode None",
+            "--outFilterMultimapNmax 50",
+            "--chimMultimapNmax 50",
+            "--quantMode GeneCounts",
+            "--outSAMunmapped Within",
+            "--readFilesCommand zcat ",
+            "--alignSJstitchMismatchNmax 5 -1 5 5",
+            "--outSAMtype BAM SortedByCoordinate",
+            "--chimSegmentMin 10",
+            "--peOverlapNbasesMin 10",
+            "--alignSplicedMateMapLminOverLmate 0.5",
+            "--chimJunctionOverhangMin 10",
+            "--chimScoreJunctionNonGTAG 0",
+            "--chimScoreDropMax 30",
+            "--chimScoreSeparation 1 ",
+            "--chimSegmentReadGapMax 3",
+            "--chimOutType Junctions WithinBAM",
+            params.star_limit_bam_sort_ram > 0 ? "--limitBAMsortRAM ${params.star_limit_bam_sort_ram}" : ""
+            ].join(' ') }
     }
 
     withName: 'STAR_GENOMEGENERATE' {

nextflow.config

@@ -47,6 +47,7 @@ params {
 
     // Alignment options
     star_ignore_sjdbgtf                  = false
+    star_limit_bam_sort_ram              = 0
     seq_center                           = ""
     seq_platform                         = ""
     fusioncatcher_limitSjdbInsertNsj     = 2000000

nextflow_schema.json

@@ -532,6 +532,12 @@
                     "hidden": true,
                     "fa_icon": "fas fa-toolbox",
                     "help_text": "Setting false will use GTF file for STAR alignment"
+                },
+                "star_limit_bam_sort_ram": {
+                    "type": "integer",
+                    "description": "The maximum amount of RAM to use for sorting the BAM file in STAR. Should by in bits. Setting this value to `0` will use the default amount of STAR.",
+                    "fa_icon": "fas fa-toolbox",
+                    "minimum": 0
                 }
             }
         }