bugfix: when there is a single input file, stageAs("?/*) returns the path directly, not in a list (#2114)

* bugfix: when there is a single input file, stageAs("?/*) returns the path directly, not in a list

* Added a test

* Added a test

* Added MD5 checksum

Co-authored-by: nvnieuwk <101190534+nvnieuwk@users.noreply.github.com>

modules/cat/fastq/main.nf

@@ -20,7 +20,7 @@ process CAT_FASTQ {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def readList = reads.collect{ it.toString() }
+    def readList = reads instanceof List ? reads.collect{ it.toString() } : [reads.toString()]
     if (meta.single_end) {
         if (readList.size >= 1) {
             """
@@ -51,7 +51,7 @@ process CAT_FASTQ {
 
     stub:
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def readList = reads.collect{ it.toString() }
+    def readList = reads instanceof List ? reads.collect{ it.toString() } : [reads.toString()]
     if (meta.single_end) {
         if (readList.size > 1) {
             """

modules/samtools/merge/main.nf

@@ -25,7 +25,7 @@ process SAMTOOLS_MERGE {
     script:
     def args = task.ext.args   ?: ''
     prefix   = task.ext.prefix ?: "${meta.id}"
-    def file_type = input_files[0].getExtension()
+    def file_type = input_files instanceof List ? input_files[0].getExtension() : input_files.getExtension()
     def reference = fasta ? "--reference ${fasta}" : ""
     """
     samtools \\
@@ -44,7 +44,7 @@ process SAMTOOLS_MERGE {
 
     stub:
     prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
-    def file_type = input_files[0].getExtension()
+    def file_type = input_files instanceof List ? input_files[0].getExtension() : input_files.getExtension()
     """
     touch ${prefix}.${file_type}
 

tests/modules/cat/fastq/main.nf

@@ -47,3 +47,12 @@ workflow test_cat_fastq_paired_end_same_name {
 
     CAT_FASTQ ( input )
 }
+
+workflow test_cat_fastq_single_end_single_file {
+    input = [
+        [ id:'test', single_end:true ], // meta map
+        [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)]
+    ]
+
+    CAT_FASTQ ( input )
+}

tests/modules/cat/fastq/test.yml

@@ -38,6 +38,15 @@
     - path: ./output/cat/test_2.merged.fastq.gz
       md5sum: fe9f266f43a6fc3dcab690a18419a56e
 
+- name: cat fastq single-end-single-file
+  command: nextflow run ./tests/modules/cat/fastq -entry test_cat_fastq_single_end_single_file -c ./tests/config/nextflow.config -c ./tests/modules/cat/fastq/nextflow.config
+  tags:
+    - cat
+    - cat/fastq
+  files:
+    - path: ./output/cat/test.merged.fastq.gz
+      md5sum: e325ef7deb4023447a1f074e285761af
+
 - name: cat fastq single-end stub
   command: nextflow run ./tests/modules/cat/fastq -entry test_cat_fastq_single_end -c ./tests/config/nextflow.config -c ./tests/modules/cat/fastq/nextflow.config -stub-run
   tags:

tests/modules/samtools/merge/main.nf

@@ -27,3 +27,13 @@ workflow test_samtools_merge_cram {
     fai   = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
     SAMTOOLS_MERGE ( input, fasta, fai )
 }
+
+workflow test_samtools_merge_single_file {
+    input = [ [ id: 'test' ], // meta map
+              [
+                file(params.test_data['sarscov2']['illumina']['test_paired_end_methylated_sorted_bam'], checkIfExists: true),
+              ]
+            ]
+
+    SAMTOOLS_MERGE ( input, [], [] )
+}

tests/modules/samtools/merge/test.yml

@@ -13,3 +13,12 @@
     - samtools/merge
   files:
     - path: output/samtools/test.cram
+
+- name: samtools merge test_samtools_merge_single_file
+  command: nextflow run ./tests/modules/samtools/merge -entry test_samtools_merge_single_file -c ./tests/config/nextflow.config -c ./tests/modules/samtools/merge/nextflow.config
+  tags:
+    - samtools
+    - samtools/merge
+  files:
+    - path: output/samtools/test.bam
+      md5sum: 6e38ae132fadae4cb4915814d6f872b2