luslab-umitools | Added index output from module

tools/umi_tools/environment.yml

@@ -7,3 +7,4 @@ channels:
   - defaults
 dependencies:
   - umi_tools=1.0.1
+  - samtools=1.1.0

tools/umi_tools/main.nf

@@ -17,7 +17,8 @@ process umitools_dedup {
         tuple val(sample_id), path(bam)
        
     output:
-        tuple val(sample_id), path("*.dedup.bam"), emit: dedupBam
+        tuple val(sample_id), path("${sample_id}.dedup.bam"), emit: dedupBam
+        tuple val(sample_id), path("${sample_id}.dedup.bam.bai"), emit: dedupBai
         path "*.dedup.log", emit: report
 
     script:
@@ -32,15 +33,16 @@ process umitools_dedup {
     }
 
     // Contruct CL line
-    command = "umi_tools dedup ${args} -I ${bam[0]} -S ${sample_id}.dedup.bam --output-stats=${sample_id}"
+    dedup_command = "umi_tools dedup ${args} -I ${bam[0]} -S ${sample_id}.dedup.bam --output-stats=${sample_id}"
 
     // Log
     if (params.verbose){
-        println ("[MODULE] umi_tools/dedup exec: " + command)
+        println ("[MODULE] umi_tools/dedup command: " + dedup_command)
     }
 
     //SHELL
     """
-    ${command}
+    ${dedup_command}
+    samtools index ${sample_id}.dedup.bam
     """
 }

tools/umi_tools/umi_tools.yml

@@ -24,12 +24,9 @@ processes:
             - sample_id:
                 type: string
                 description: Sample identifier
-            - bai:
-                type: file
-                description: BAM file index
             - bam:
-                type: file
-                description: BAM sequence file
+                type: file array
+                description: BAM sequence file and associated BAI index file
         output:
             - dedupBam:
                 type: tuple