Add back RSEM support for IHEC profile

guigolab · May 3, 2024 · e72b889 · e72b889
1 parent 39f14d1
commit e72b889
Showing 1 changed file with 6 additions and 3 deletions.
diff --git a/modules/quantification/rsem/main.nf b/modules/quantification/rsem/main.nf
@@ -91,11 +91,14 @@ process calculateExpression {
     def cmd = []
     if ( convertBam ) {
         rsemPrefix = "${rsemPrefix}.rsem"
-        def convertMemory = Math.max(1024, ( memory / task.cpus / 2 ) as long)
+        def convertOpts = ""
+        if ( params.rsemVersion.startsWith("1.3") && ( ! params.container.contains("ihec") ) ) {
+            def convertMemory = Math.max(1024, ( memory / task.cpus / 2 ) as long)
+            convertOpts = "-p ${task.cpus} --memory-per-thread ${convertMemory}M"
+        }
         cmd << """\
             mkfifo ${rsemPrefix}.bam
-            convert-sam-for-rsem -p ${task.cpus} \\
-                                 --memory-per-thread ${convertMemory}M \\
+            convert-sam-for-rsem ${convertOpts} \\
                                  ${bam} \\
                                  ${rsemPrefix} &
         """.stripIndent()