From a1c7ed2affc9797fe68d353db09a75296357b86c Mon Sep 17 00:00:00 2001
From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com>
Date: Mon, 31 Jul 2023 15:36:50 +0200
Subject: [PATCH 1/2] update markduplicates default prefix

---
 conf/modules/align.config | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/conf/modules/align.config b/conf/modules/align.config
index 249dc81e..54dae858 100644
--- a/conf/modules/align.config
+++ b/conf/modules/align.config
@@ -19,8 +19,9 @@ process{
     }
 
     withName: '.*ALIGN:SAMTOOLS_VIEW' {
-        ext.args = { '--output-fmt cram --write-index' }
-        ext.when = params.save_mapped_as_cram
+        ext.args   = { '--output-fmt cram --write-index' }
+        ext.prefix = { "${meta.id}_sorted_md" }
+        ext.when   = params.save_mapped_as_cram
         publishDir = [
             path: { "${params.outdir}/alignment" },
             mode: params.publish_dir_mode,

From 7817473c5efa4ea841f8c89ac731a8e0d059b632 Mon Sep 17 00:00:00 2001
From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com>
Date: Mon, 31 Jul 2023 15:49:27 +0200
Subject: [PATCH 2/2] update changelog

---
 CHANGELOG.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 7399915b..ab9e831b 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -16,6 +16,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### `Fixed`
 
 - Invalid GATK4 container which caused incorrect singularity downloads with nf-core download [nf-core/modules #3668](https://github.com/nf-core/modules/issues/3668)
+- Make the default cram prefix same as markduplicates prefix [#392](https://github.com/nf-core/raredisease/pull/392)
 
 ## v1.1.1 - Abu (Patch) [2023-07-26]