From c4212df1b3986421e14285d256f828c5d7e1e17a Mon Sep 17 00:00:00 2001
From: Kelly Sovacool <kelly.sovacool@nih.gov>
Date: Thu, 19 Oct 2023 16:24:50 -0400
Subject: [PATCH] feat: index bam

---
 modules/CCBR/samtools/filter_aligned/main.nf | 9 ++++++---
 1 file changed, 6 insertions(+), 3 deletions(-)

diff --git a/modules/CCBR/samtools/filter_aligned/main.nf b/modules/CCBR/samtools/filter_aligned/main.nf
index 71ac52b..8f0cc8a 100644
--- a/modules/CCBR/samtools/filter_aligned/main.nf
+++ b/modules/CCBR/samtools/filter_aligned/main.nf
@@ -12,8 +12,8 @@ process FILTER_ALIGNED {
         tuple val(meta), path(bam), path(bai)
 
     output:
-        tuple val(meta), path("*.unaligned.bam"), emit: bam
-        path  "versions.yml"                    , emit: versions
+        tuple val(meta), path("*.unaligned.bam"), path('*.unaligned.bam.bai'), emit: bam
+        path  "versions.yml"                                                 , emit: versions
 
     when:
         task.ext.when == null || task.ext.when
@@ -28,6 +28,9 @@ process FILTER_ALIGNED {
       -b \\
       -o ${prefix}.unaligned.bam \\
       ${prefix}.bam
+    samtools index \\
+      -@ ${task.cpus} \\
+      ${prefix}.unaligned.bam
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
@@ -37,6 +40,6 @@ process FILTER_ALIGNED {
 
     stub:
     """
-    touch ${meta.id}.unaligned.bam versions.yml
+    touch ${meta.id}.unaligned.bam ${meta.id}.unaligned.bam.bai versions.yml
     """
 }