Adding input value-channel for controlling spring-decompress cmd and output

modules/nf-core/spring/decompress/main.nf

@@ -9,6 +9,7 @@ process SPRING_DECOMPRESS {
 
     input:
     tuple val(meta), path(spring)
+    val(write_one_fastq_gz)
 
     output:
     tuple val(meta), path("*.fastq.gz"), emit: fastq
@@ -21,7 +22,7 @@ process SPRING_DECOMPRESS {
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     def VERSION = '1.1.1' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
-    def output = meta.single_end ? "-o ${prefix}.fastq.gz" : "-o ${prefix}_R1.fastq.gz ${prefix}_R2.fastq.gz"
+    def output = write_one_fastq_gz ? "-o ${prefix}.fastq.gz" : "-o ${prefix}_R1.fastq.gz ${prefix}_R2.fastq.gz"
 
     """
     spring \\

modules/nf-core/spring/decompress/meta.yml

@@ -22,6 +22,10 @@ input:
       type: file
       description: Spring file to decompress.
       pattern: "*.{spring}"
+  - write_one_fastq_gz:
+      type: boolean
+      description: Controls whether spring should write one fastq.gz file with reads from both directions or two fastq.gz files with reads from distinct directions
+      pattern: "true or false"
 output:
   - meta:
       type: map

tests/modules/nf-core/spring/decompress/main.nf

@@ -8,23 +8,23 @@ include { SPRING_DECOMPRESS } from '../../../../../modules/nf-core/spring/decomp
 workflow test_spring_decompress_single_end {
 
     input = [
-        [ id:'test', single_end:true ], // meta map
+        [ id:'test' ], // meta map
         file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
         []
     ]
 
     SPRING_COMPRESS ( input )
-    SPRING_DECOMPRESS ( SPRING_COMPRESS.out.spring )
+    SPRING_DECOMPRESS ( SPRING_COMPRESS.out.spring, true )
 }
 
 workflow test_spring_decompress_paired_end {
 
     input = [
-        [ id:'test', single_end:false ], // meta map
+        [ id:'test' ], // 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)
     ]
 
     SPRING_COMPRESS ( input )
-    SPRING_DECOMPRESS ( SPRING_COMPRESS.out.spring )
+    SPRING_DECOMPRESS ( SPRING_COMPRESS.out.spring, false )
 }