From 0d660098f00c51859ceb1bb32444f0f8ad139918 Mon Sep 17 00:00:00 2001
From: Alexander Koc <alexander.koc@skane.se>
Date: Wed, 20 Dec 2023 14:30:10 +0100
Subject: [PATCH 1/3] Fix missing/wrong sentieon dedup stub output files

The files output by the process stub now match that of the main process.

The stub also creates a bam/cram bai/crai file depending on the process
input, instead of just creating a cram and crai by default.
---
 modules/nf-core/sentieon/dedup/main.nf | 11 ++++++-----
 1 file changed, 6 insertions(+), 5 deletions(-)

diff --git a/modules/nf-core/sentieon/dedup/main.nf b/modules/nf-core/sentieon/dedup/main.nf
index 01ee885a177..1204ad512b6 100644
--- a/modules/nf-core/sentieon/dedup/main.nf
+++ b/modules/nf-core/sentieon/dedup/main.nf
@@ -89,15 +89,16 @@ process SENTIEON_DEDUP {
     } else {
         fix_ld_library_path = ''
     }
-
     def prefix = task.ext.prefix ?: "${meta.id}"
+    def suffix = task.ext.suffix ?: ".cram"   // The suffix should be either ".cram" or ".bam".
+    def metrics = task.ext.metrics ?: "${prefix}${suffix}.metrics"
     """
     $fix_ld_library_path
 
-    touch ${prefix}.cram
-    touch ${prefix}.cram.crai
-    touch ${prefix}.metrics
-    touch ${prefix}.score
+    touch "${prefix}${suffix}\$(echo ${suffix} | sed 's/m\$/i/')"
+    touch "${metrics}"
+    touch "${metrics}.multiqc.tsv"
+    touch "${prefix}.score"
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

From 1d97ce1249e1585e4fd63f12eca639930c5766fc Mon Sep 17 00:00:00 2001
From: Alexander Koc <alexander.koc@skane.se>
Date: Wed, 20 Dec 2023 14:56:09 +0100
Subject: [PATCH 2/3] Create bam/crai stub file

---
 modules/nf-core/sentieon/dedup/main.nf | 1 +
 1 file changed, 1 insertion(+)

diff --git a/modules/nf-core/sentieon/dedup/main.nf b/modules/nf-core/sentieon/dedup/main.nf
index 1204ad512b6..0679a20d4b0 100644
--- a/modules/nf-core/sentieon/dedup/main.nf
+++ b/modules/nf-core/sentieon/dedup/main.nf
@@ -95,6 +95,7 @@ process SENTIEON_DEDUP {
     """
     $fix_ld_library_path
 
+    touch "${prefix}${suffix}""
     touch "${prefix}${suffix}\$(echo ${suffix} | sed 's/m\$/i/')"
     touch "${metrics}"
     touch "${metrics}.multiqc.tsv"

From 058fa2cb66692e3877e36be831722f492fe22509 Mon Sep 17 00:00:00 2001
From: Alexander Koc <alexander.koc@skane.se>
Date: Wed, 20 Dec 2023 15:03:39 +0100
Subject: [PATCH 3/3] Fix extra quotation mark x_x

---
 modules/nf-core/sentieon/dedup/main.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/nf-core/sentieon/dedup/main.nf b/modules/nf-core/sentieon/dedup/main.nf
index 0679a20d4b0..316993cc158 100644
--- a/modules/nf-core/sentieon/dedup/main.nf
+++ b/modules/nf-core/sentieon/dedup/main.nf
@@ -95,7 +95,7 @@ process SENTIEON_DEDUP {
     """
     $fix_ld_library_path
 
-    touch "${prefix}${suffix}""
+    touch "${prefix}${suffix}"
     touch "${prefix}${suffix}\$(echo ${suffix} | sed 's/m\$/i/')"
     touch "${metrics}"
     touch "${metrics}.multiqc.tsv"