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

…output (#5850) * Enable single fastq.gz-output from spring/decompress by setting meta.single_end or meta.one_strand * Controlling output with value-channel write_one_fastq_gz * Update modules/nf-core/spring/decompress/meta.yml Co-authored-by: Maxime U Garcia <[email protected]> * nf-test for spring/decompress * Trying to please linter * Trying to please linter --------- Co-authored-by: Simon Pearce <[email protected]> Co-authored-by: Maxime U Garcia <[email protected]>
nf-core · Jun 23, 2024 · 0a92fa8 · 0a92fa8
1 parent db35d26
commit 0a92fa8
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diff --git a/modules/nf-core/spring/decompress/main.nf b/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 \\

diff --git a/modules/nf-core/spring/decompress/meta.yml b/modules/nf-core/spring/decompress/meta.yml
@@ -11,7 +11,7 @@ tools:
       documentation: "https://github.com/shubhamchandak94/Spring/blob/master/README.md"
       tool_dev_url: "https://github.com/shubhamchandak94/Spring"
       doi: "10.1093/bioinformatics/bty1015"
-      licence: "['Free for non-commercial use']"
+      licence: ["Free for non-commercial use"]
 input:
   - meta:
       type: map
@@ -22,6 +22,11 @@ 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

diff --git a/modules/nf-core/spring/decompress/test/main.nf.test b/modules/nf-core/spring/decompress/test/main.nf.test
@@ -0,0 +1,78 @@
+nextflow_process {
+
+    name "Test Process SPRING_DECOMPRESS"
+    tag "modules_nfcore"
+    tag "modules"
+    tag "spring"
+    tag "spring/decompress"
+    script "../main.nf"
+    process "SPRING_DECOMPRESS"
+
+    test("Write-One-File") {
+
+        setup {
+            run("SPRING_COMPRESS") {
+                script "../../compress/main.nf"
+                process {
+                    """
+                    input[0] = [
+                        [ id:'test' ], // meta map
+                        file(params.modules_testdata_base_path + '/genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
+                        []
+                    ]
+                    """
+                }
+            }
+        }
+
+        when {
+            process {
+                """
+                input[0] = SPRING_COMPRESS.out.spring
+                input[1] = true // write_one_fastq_gz
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("Write-Two-Files") {
+
+        setup {
+            run("SPRING_COMPRESS") {
+                script "../../compress/main.nf"
+                process {
+                    """
+                    input[0] = [
+                        [ id:'test2' ], // meta map
+                        file(params.modules_testdata_base_path + '/genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
+                        file(params.modules_testdata_base_path + '/genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true),
+                    ]
+                    """
+                }
+            }
+        }
+
+        when {
+            process {
+                """
+                input[0] = SPRING_COMPRESS.out.spring
+                input[1] = false // write_one_fastq_gz
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+}
diff --git a/modules/nf-core/spring/decompress/test/main.nf.test.snap b/modules/nf-core/spring/decompress/test/main.nf.test.snap
@@ -0,0 +1,74 @@
+{
+    "Write-Two-Files": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test2"
+                        },
+                        [
+                            "test2_R1.fastq.gz:md5,4161df271f9bfcd25d5845a1e220dbec",
+                            "test2_R2.fastq.gz:md5,2ebae722295ea66d84075a3b042e2b42"
+                        ]
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,4711df5941f1464e3693d24dd29c705b"
+                ],
+                "fastq": [
+                    [
+                        {
+                            "id": "test2"
+                        },
+                        [
+                            "test2_R1.fastq.gz:md5,4161df271f9bfcd25d5845a1e220dbec",
+                            "test2_R2.fastq.gz:md5,2ebae722295ea66d84075a3b042e2b42"
+                        ]
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,4711df5941f1464e3693d24dd29c705b"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-06-21T13:41:46.090761471"
+    },
+    "Write-One-File": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.fastq.gz:md5,4161df271f9bfcd25d5845a1e220dbec"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,4711df5941f1464e3693d24dd29c705b"
+                ],
+                "fastq": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.fastq.gz:md5,4161df271f9bfcd25d5845a1e220dbec"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,4711df5941f1464e3693d24dd29c705b"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-06-21T13:02:07.466039653"
+    }
+}
diff --git a/modules/nf-core/spring/decompress/test/nextflow.config b/modules/nf-core/spring/decompress/test/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/modules/nf-core/spring/decompress/test/tags.yml b/modules/nf-core/spring/decompress/test/tags.yml
@@ -0,0 +1,3 @@
+spring/decompress:
+  - modules/nf-core/spring/compress/**
+  - modules/nf-core/spring/decompress/**
diff --git a/tests/modules/nf-core/spring/decompress/main.nf b/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 )
 }