address review comments

modules/biobambam/bammerge/main.nf

@@ -12,7 +12,9 @@ process BIOBAMBAM_BAMMERGE {
 
     output:
     tuple val(meta), path("${prefix}.bam")    ,emit: bam
-    tuple val(meta), path("*.bam.bai")        ,optional:true, emit: bam_index
+    tuple val(meta), path("${indexfilename}") ,optional:true, emit: bam_index
+    tuple val(meta), path("${md5filename}")   ,optional:true, emit: checksum
+
     path "versions.yml"                       ,emit: versions
 
     when:
@@ -21,6 +23,8 @@ process BIOBAMBAM_BAMMERGE {
     script:
     def args = task.ext.args ?: ''
     prefix = task.ext.prefix ?: "${meta.id}"
+    indexfilename = args.contains("indexfilename=") ? args =~ /indexfilename=([^\s]+)/ : ""
+    md5filename = args.contains("md5filename=") ? args =~ /md5filename=([^\s]+)/ : ""
     def input_string = bam.join(" I=")
 
     """
@@ -31,7 +35,7 @@ process BIOBAMBAM_BAMMERGE {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        bammerge: \$( bammerge --version |& sed '1!d; s/.*version //; s/.$//' )
+        bammerge: \$( bammerge --version |& sed '1!d; s/.*version //; s/.\$//' )
     END_VERSIONS
     """
 }

modules/biobambam/bammerge/meta.yml

@@ -33,7 +33,11 @@ output:
   - bam_index:
       type: file
       description: BAM index file
-      pattern: "*.{bai}"
+      pattern: "*"
+  - checksum:
+      type: file
+      description: Checksum file
+      pattern: "*"
   - versions:
       type: file
       description: File containing software versions

tests/modules/biobambam/bammerge/main.nf

@@ -4,7 +4,7 @@ nextflow.enable.dsl = 2
 
 include { BIOBAMBAM_BAMMERGE } from '../../../../modules/biobambam/bammerge/main.nf'
 
-workflow test_biobambam_bammerge {
+workflow test_biobambam_bammerge_paired {
 
     input = [
         [ id:'test', single_end:false ], // meta map
@@ -16,3 +16,15 @@ workflow test_biobambam_bammerge {
 
     BIOBAMBAM_BAMMERGE ( input )
 }
+
+workflow test_biobambam_bammerge_single {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        [
+            file(params.test_data['sarscov2']['illumina']['test_single_end_sorted_bam'], checkIfExists: true),
+        ]
+    ]
+
+    BIOBAMBAM_BAMMERGE ( input )
+}

tests/modules/biobambam/bammerge/nextflow.config

@@ -1,5 +1,8 @@
 process {
 
     publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+    withName: BIOBAMBAM_BAMMERGE {
+        ext.args = "md5=1 md5filename=test.md5 index=1 indexfilename=test.bam.bai"
+    }
 
 }

tests/modules/biobambam/bammerge/test.yml

@@ -1,8 +1,17 @@
-- name: biobambam bammerge test_biobambam_bammerge
-  command: nextflow run ./tests/modules/biobambam/bammerge -entry test_biobambam_bammerge -c ./tests/config/nextflow.config  -c ./tests/modules/biobambam/bammerge/nextflow.config
+- name: biobambam bammerge test_biobambam_bammerge_paired
+  command: nextflow run ./tests/modules/biobambam/bammerge -entry test_biobambam_bammerge_paired -c ./tests/config/nextflow.config  -c ./tests/modules/biobambam/bammerge/nextflow.config
   tags:
-    - biobambam/bammerge
     - biobambam
+    - biobambam/bammerge
   files:
     - path: output/biobambam/test.bam
-      md5sum: 676157f300c774a58dd3b7b554e00f11
+      md5sum: bc3d32ab6a54d1894ca7cc79387dec57
+
+- name: biobambam bammerge test_biobambam_bammerge_single
+  command: nextflow run ./tests/modules/biobambam/bammerge -entry test_biobambam_bammerge_single -c ./tests/config/nextflow.config  -c ./tests/modules/biobambam/bammerge/nextflow.config
+  tags:
+    - biobambam
+    - biobambam/bammerge
+  files:
+    - path: output/biobambam/test.bam
+      md5sum: 86185d3d6895a7722d3b3a09c6f91bfc