From e72b8897132b1ba141a2f48d5c77eaf05793512c Mon Sep 17 00:00:00 2001
From: Emilio Palumbo <emiliopalumbo@gmail.com>
Date: Fri, 3 May 2024 17:19:27 +0200
Subject: [PATCH] Add back RSEM support for IHEC profile

---
 modules/quantification/rsem/main.nf | 9 ++++++---
 1 file changed, 6 insertions(+), 3 deletions(-)

diff --git a/modules/quantification/rsem/main.nf b/modules/quantification/rsem/main.nf
index d0df9e9..3bb15f3 100644
--- 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()