Add parameter for setting STAR limitSjdbInsertNsj

nf-core · Apr 15, 2024 · 1c9d74e · 1c9d74e
1 parent d4199c4
commit 1c9d74e
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Showing 3 changed files with 14 additions and 0 deletions.
diff --git a/conf/modules.config b/conf/modules.config
@@ -197,6 +197,7 @@ if (!params.skip_trimming) {
             "--outReadsUnmapped None",
             "--readFilesCommand zcat",
             "--alignSJDBoverhangMin ${params.alignSJDBoverhangMin}",
+            "--limitSjdbInsertNsj ${params.limitSjdbInsertNsj}",
             "--chimJunctionOverhangMin ${params.chimJunctionOverhangMin}",
             "--chimSegmentMin ${params.chimSegmentMin}"
         ].join(' ').trim()
@@ -228,6 +229,7 @@ if (!params.skip_trimming) {
             "--readFilesCommand zcat",
             "--sjdbFileChrStartEnd dataset.SJ.out.tab",
             "--alignSJDBoverhangMin ${params.alignSJDBoverhangMin}",
+            "--limitSjdbInsertNsj ${params.limitSjdbInsertNsj}",
             "--chimJunctionOverhangMin ${params.chimJunctionOverhangMin}",
             "--chimSegmentMin ${params.chimSegmentMin}"
         ].join(' ').trim()
@@ -395,6 +397,7 @@ if (!params.skip_trimming) {
             "--outReadsUnmapped None",
             "--readFilesCommand zcat",
             "--alignSJDBoverhangMin ${params.alignSJDBoverhangMin}",
+            "--limitSjdbInsertNsj ${params.limitSjdbInsertNsj}",
             "--chimJunctionOverhangMin ${params.chimJunctionOverhangMin}",
             "--chimSegmentMin ${params.chimSegmentMin}"
         ].join(' ').trim()
@@ -426,6 +429,7 @@ if (!params.skip_trimming) {
             "--readFilesCommand zcat",
             "--sjdbFileChrStartEnd dataset.SJ.out.tab",
             "--alignSJDBoverhangMin ${params.alignSJDBoverhangMin}",
+            "--limitSjdbInsertNsj ${params.limitSjdbInsertNsj}",
             "--chimJunctionOverhangMin ${params.chimJunctionOverhangMin}",
             "--chimSegmentMin ${params.chimSegmentMin}"
         ].join(' ').trim()
@@ -447,6 +451,7 @@ if (!params.skip_trimming) {
             "--outReadsUnmapped None",
             "--readFilesCommand zcat",
             "--alignSJDBoverhangMin ${params.alignSJDBoverhangMin}",
+            "--limitSjdbInsertNsj ${params.limitSjdbInsertNsj}",
             "--chimJunctionOverhangMin ${params.chimJunctionOverhangMin}",
             "--chimSegmentMin ${params.chimSegmentMin}"
         ].join(' ').trim()
@@ -479,6 +484,7 @@ if (!params.skip_trimming) {
             "--readFilesCommand zcat",
             "--sjdbFileChrStartEnd dataset.SJ.out.tab",
             "--alignSJDBoverhangMin ${params.alignSJDBoverhangMin}",
+            "--limitSjdbInsertNsj ${params.limitSjdbInsertNsj}",
             "--chimJunctionOverhangMin ${params.chimJunctionOverhangMin}",
             "--chimSegmentMin ${params.chimSegmentMin}"
         ].join(' ').trim()
@@ -500,6 +506,7 @@ if (!params.skip_trimming) {
             "--outReadsUnmapped None",
             "--readFilesCommand zcat",
             "--alignSJDBoverhangMin ${params.alignSJDBoverhangMin}",
+            "--limitSjdbInsertNsj ${params.limitSjdbInsertNsj}",
             "--chimJunctionOverhangMin ${params.chimJunctionOverhangMin}",
             "--chimSegmentMin ${params.chimSegmentMin}"
         ].join(' ').trim()
@@ -532,6 +539,7 @@ if (!params.skip_trimming) {
             "--readFilesCommand zcat",
             "--sjdbFileChrStartEnd dataset.SJ.out.tab",
             "--alignSJDBoverhangMin ${params.alignSJDBoverhangMin}",
+            "--limitSjdbInsertNsj ${params.limitSjdbInsertNsj}",
             "--chimJunctionOverhangMin ${params.chimJunctionOverhangMin}",
             "--chimSegmentMin ${params.chimSegmentMin}"
         ].join(' ').trim()

diff --git a/nextflow.config b/nextflow.config
@@ -54,6 +54,7 @@ params {
     alignSJDBoverhangMin       = 10
     chimSegmentMin             = 10
     sjdboverhang               = 100
+    limitSjdbInsertNsj         = 1000000
 
     //> MAPSPLICE
     seglen                     = 25

diff --git a/nextflow_schema.json b/nextflow_schema.json
@@ -125,6 +125,11 @@
                     "description": "Minimum overhang for annotated junctions",
                     "default": 10
                 },
+                "limitSjdbInsertNsj": {
+                    "type": "integer",
+                    "description": "Maximum number of junction to be inserted to the genome on the fly at the mapping stage, including those from annotations and those detected in the 1st step of the 2-pass run",
+                    "default": 1000000
+                },
                 "chimSegmentMin": {
                     "type": "integer",
                     "description": "Minimum length of chimeric segment length. Must be set to a positive value to detect circular junctions.",