From 541006fc0d41ceff2c974028ffb87dbb4ad33225 Mon Sep 17 00:00:00 2001
From: vidboda <david.baux@inserm.fr>
Date: Thu, 26 Sep 2024 18:16:19 +0200
Subject: [PATCH] descattered recalbams & leftalign

---
 modules/gatkLeftAlignIndels.wdl | 2 +-
 panelCapture.wdl                | 4 ++--
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/modules/gatkLeftAlignIndels.wdl b/modules/gatkLeftAlignIndels.wdl
index 17abaf7..ca57cf0 100644
--- a/modules/gatkLeftAlignIndels.wdl
+++ b/modules/gatkLeftAlignIndels.wdl
@@ -46,7 +46,7 @@ task gatkLeftAlignIndels {
 	}
 	output {
 		File lAlignedBam = "~{OutDir}~{OutputDirSampleID}/~{WorkflowType}/~{SampleID}.dupmarked.recal.laligned.bam"
-		File lAlignedBamIndex = "~{OutDir}~{OutputDirSampleID}/~{WorkflowType}/recal_bams/~{SampleID}.dupmarked.recal.laligned.bai"
+		File lAlignedBamIndex = "~{OutDir}~{OutputDirSampleID}/~{WorkflowType}/~{SampleID}.dupmarked.recal.laligned.bai"
 		# File lAlignedBam = "~{OutDir}~{OutputDirSampleID}/~{WorkflowType}/recal_bams/~{SampleID}.~{IntervalName}.dupmarked.recal.laligned.bam"
 		# File lAlignedBamIndex = "~{OutDir}~{OutputDirSampleID}/~{WorkflowType}/recal_bams/~{SampleID}.~{IntervalName}.dupmarked.recal.laligned.bai"
 	}
diff --git a/panelCapture.wdl b/panelCapture.wdl
index c4bb2c7..9962a3f 100755
--- a/panelCapture.wdl
+++ b/panelCapture.wdl
@@ -312,7 +312,7 @@ workflow panelCapture {
 		input:
 			Queue = defQueue,
 			Cpu = cpuLow,
-			Memory = memoryLow,
+			Memory = memoryHigh,
 			SampleID = sampleID,
 			OutDir = outDir,
 			WorkflowType = workflowType,
@@ -329,7 +329,7 @@ workflow panelCapture {
 		input:
 			Queue = defQueue,
 			Cpu = cpuLow,
-			Memory = memoryLow,
+			Memory = memoryHigh,
 			SampleID = sampleID,
 			OutDir = outDir,
 			WorkflowType = workflowType,