3630 add unstitched reads as emitted output of ngmerge (nf-core#3632)

* add -f option * update tests
SusiJo · Jul 12, 2023 · 61aa491 · 61aa491
1 parent 30d06da
commit 61aa491
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Showing 4 changed files with 24 additions and 13 deletions.
diff --git a/modules/nf-core/ngmerge/main.nf b/modules/nf-core/ngmerge/main.nf
@@ -8,10 +8,12 @@ process NGMERGE {
         'biocontainers/ngmerge:0.3--ha92aebf_1' }"
 
     input:
-    tuple val(meta), path(reads1), path(reads2)
+    tuple val(meta), path(reads)
 
     output:
     tuple val(meta), path("*.merged.fq.gz"), emit: merged_reads
+    tuple val(meta), path("*_1.fastq.gz")  , emit: unstitched_read1
+    tuple val(meta), path("*_2.fastq.gz")  , emit: unstitched_read2
     path "versions.yml"                    , emit: versions
 
     when:
@@ -23,9 +25,10 @@ process NGMERGE {
 
     """
     NGmerge \\
-        -1 $reads1 \\
-        -2 $reads2 \\
+        -1 ${reads[0]} \\
+        -2 ${reads[1]} \\
         -o ${prefix}.merged.fq.gz \\
+        -f ${prefix}_unstitched \\
         -z \\
         -n $task.cpus \\
         $args

diff --git a/modules/nf-core/ngmerge/meta.yml b/modules/nf-core/ngmerge/meta.yml
@@ -22,14 +22,10 @@ input:
         Groovy Map containing sample information
         e.g. `[ id:'test', single_end:false ]`
 
-  - reads1:
+  - reads:
       type: file
-      description: fastq file paired end read 1
-      pattern: "*.{fa,fasta,fastq,fq,fa.gz,fasta.gz,fastq.gz,fq.gz}"
-
-  - reads2:
-      type: file
-      description: fastq file paired end read 2
+      description: |
+        List of input FastQ files of size 2; i.e., paired-end data.
       pattern: "*.{fa,fasta,fastq,fq,fa.gz,fasta.gz,fastq.gz,fq.gz}"
 
 output:
@@ -46,7 +42,17 @@ output:
 
   - merged_reads:
       type: file
-      description: fastq file paired end read 2
+      description: fastq file merged reads
+      pattern: "*.{fa,fasta,fastq,fq,fa.gz,fasta.gz,fastq.gz,fq.gz}"
+
+  - unstitched_read1:
+      type: file
+      description: fastq file unstitched read 1
+      pattern: "*.{fa,fasta,fastq,fq,fa.gz,fasta.gz,fastq.gz,fq.gz}"
+
+  - unstitched_read2:
+      type: file
+      description: fastq file unstitched read 2
       pattern: "*.{fa,fasta,fastq,fq,fa.gz,fasta.gz,fastq.gz,fq.gz}"
 
 authors:

diff --git a/tests/modules/nf-core/ngmerge/main.nf b/tests/modules/nf-core/ngmerge/main.nf
@@ -7,8 +7,8 @@ include { NGMERGE } from '../../../../modules/nf-core/ngmerge/main.nf'
 workflow test_ngmerge {
     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)]
     ]
 
     NGMERGE ( input )

diff --git a/tests/modules/nf-core/ngmerge/test.yml b/tests/modules/nf-core/ngmerge/test.yml
@@ -4,4 +4,6 @@
     - ngmerge
   files:
     - path: output/ngmerge/test.merged.fq.gz
+    - path: output/ngmerge/test_unstitched_1.fastq.gz
+    - path: output/ngmerge/test_unstitched_2.fastq.gz
     - path: output/ngmerge/versions.yml