bamsormadup: add extra test case, fix single file input (#1905)

modules/biobambam/bamsormadup/main.nf

@@ -22,8 +22,7 @@ process BIOBAMBAM_BAMSORMADUP {
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     def suffix = args.contains("outputformat=cram") ? "cram" : "bam"
-    def input_string = bams.join(" I=")
-
+    def input_string = bams instanceof List ? bams.join(" I=") : bams
     if (args.contains("outputformat=cram") && reference == null) error "Reference required for CRAM output."
 
     """

tests/modules/biobambam/bamsormadup/main.nf

@@ -4,7 +4,7 @@ nextflow.enable.dsl = 2
 
 include { BIOBAMBAM_BAMSORMADUP } from '../../../../modules/biobambam/bamsormadup/main.nf'
 
-workflow test_biobambam_bamsormadup {
+workflow test_biobambam_bamsormadup_multi_input {
 
     input = [
         [ id:'test', single_end:false ], // meta map
@@ -13,3 +13,13 @@ workflow test_biobambam_bamsormadup {
 
     BIOBAMBAM_BAMSORMADUP ( input, [] )
 }
+
+workflow test_biobambam_bamsormadup_single_input {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        [file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)],
+    ]
+
+    BIOBAMBAM_BAMSORMADUP ( input, [] )
+}

tests/modules/biobambam/bamsormadup/test.yml

@@ -1,5 +1,5 @@
-- name: biobambam bamsormadup test_biobambam_bamsormadup
-  command: nextflow run ./tests/modules/biobambam/bamsormadup -entry test_biobambam_bamsormadup -c ./tests/config/nextflow.config  -c ./tests/modules/biobambam/bamsormadup/nextflow.config
+- name: biobambam bamsormadup test_biobambam_bamsormadup_multi_input
+  command: nextflow run ./tests/modules/biobambam/bamsormadup -entry test_biobambam_bamsormadup_multi_input -c ./tests/config/nextflow.config  -c ./tests/modules/biobambam/bamsormadup/nextflow.config
   tags:
     - biobambam
     - biobambam/bamsormadup
@@ -8,3 +8,14 @@
       md5sum: 1d549a00b065584c298594180ca9f3bc
     - path: output/biobambam/test.metrics.txt
       md5sum: 1721879bea1f3888ecd33b35e6ee0e72
+
+- name: biobambam bamsormadup test_biobambam_bamsormadup_single_input
+  command: nextflow run ./tests/modules/biobambam/bamsormadup -entry test_biobambam_bamsormadup_single_input -c ./tests/config/nextflow.config  -c ./tests/modules/biobambam/bamsormadup/nextflow.config
+  tags:
+    - biobambam
+    - biobambam/bamsormadup
+  files:
+    - path: output/biobambam/test.bam
+      md5sum: 48e01431daec7fb17471d930a6d1d587
+    - path: output/biobambam/test.metrics.txt
+      md5sum: b97458eff0d4b259055e4902849ee53b