Stage fastq for concat in subfolders to avoid name collision issue (#1107)

* Stage fastq for concat in subfolders in task workdir

* Update main.nf

* Update test.yml

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

modules/cat/fastq/main.nf

@@ -8,7 +8,7 @@ process CAT_FASTQ {
         'biocontainers/biocontainers:v1.2.0_cv1' }"
 
     input:
-    tuple val(meta), path(reads)
+    tuple val(meta), path(reads, stageAs: "input*/*")
 
     output:
     tuple val(meta), path("*.merged.fastq.gz"), emit: reads
@@ -21,7 +21,7 @@ process CAT_FASTQ {
     if (meta.single_end) {
         if (readList.size > 1) {
             """
-            cat ${readList.sort().join(' ')} > ${prefix}.merged.fastq.gz
+            cat ${readList.join(' ')} > ${prefix}.merged.fastq.gz
 
             cat <<-END_VERSIONS > versions.yml
             "${task.process}":
@@ -35,8 +35,8 @@ process CAT_FASTQ {
             def read2 = []
             readList.eachWithIndex{ v, ix -> ( ix & 1 ? read2 : read1 ) << v }
             """
-            cat ${read1.sort().join(' ')} > ${prefix}_1.merged.fastq.gz
-            cat ${read2.sort().join(' ')} > ${prefix}_2.merged.fastq.gz
+            cat ${read1.join(' ')} > ${prefix}_1.merged.fastq.gz
+            cat ${read2.join(' ')} > ${prefix}_2.merged.fastq.gz
 
             cat <<-END_VERSIONS > versions.yml
             "${task.process}":

tests/modules/cat/fastq/main.nf

@@ -25,3 +25,25 @@ workflow test_cat_fastq_paired_end {
 
     CAT_FASTQ ( input )
 }
+
+workflow test_cat_fastq_single_end_same_name {
+    input = [
+        [ id:'test', single_end:true ], // meta map
+        [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
+        file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]
+    ]
+
+    CAT_FASTQ ( input )
+}
+
+workflow test_cat_fastq_paired_end_same_name {
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
+        file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true),
+        file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
+        file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
+    ]
+
+    CAT_FASTQ ( input )
+}

tests/modules/cat/fastq/test.yml

@@ -5,7 +5,7 @@
     - cat/fastq
   files:
     - path: ./output/cat/test.merged.fastq.gz
-      md5sum: 59f6dbe193741bb40f498f254aeb2e99
+      md5sum: f9cf5e375f7de81a406144a2c70cc64d
 
 - name: cat fastq fastqc_paired_end
   command: nextflow run ./tests/modules/cat/fastq -entry test_cat_fastq_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/cat/fastq/nextflow.config
@@ -14,6 +14,26 @@
     - cat/fastq
   files:
     - path: ./output/cat/test_2.merged.fastq.gz
-      md5sum: d2b1a836eef1058738ecab36c907c5ba
+      md5sum: 77c8e966e130d8c6b6ec9be52fcb2bda
     - path: ./output/cat/test_1.merged.fastq.gz
-      md5sum: 59f6dbe193741bb40f498f254aeb2e99
+      md5sum: f9cf5e375f7de81a406144a2c70cc64d
+
+- name: cat fastq single-end-same-name
+  command: nextflow run ./tests/modules/cat/fastq -entry test_cat_fastq_single_end_same_name -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: 63f817db7a29a03eb538104495556f66
+
+- name: cat fastq fastqc_paired_end_same_name
+  command: nextflow run ./tests/modules/cat/fastq -entry test_cat_fastq_paired_end_same_name -c ./tests/config/nextflow.config -c ./tests/modules/cat/fastq/nextflow.config
+  tags:
+    - cat
+    - cat/fastq
+  files:
+    - path: ./output/cat/test_1.merged.fastq.gz
+      md5sum: 63f817db7a29a03eb538104495556f66
+    - path: ./output/cat/test_2.merged.fastq.gz
+      md5sum: fe9f266f43a6fc3dcab690a18419a56e