migrating flash to nf-test (#5470)

* migrating flash to nf-test * removing args2 from main.nf * Update nextflow.config * Changes discussed in the outputs --------- Co-authored-by: Simon Pearce <[email protected]>
nf-core · Apr 29, 2024 · 4db86a0 · 4db86a0
1 parent e0616fb
commit 4db86a0
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Showing 10 changed files with 157 additions and 42 deletions.
diff --git a/modules/nf-core/flash/main.nf b/modules/nf-core/flash/main.nf
@@ -4,22 +4,28 @@ process FLASH {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/flash:1.2.11--hed695b0_5' :
-        'biocontainers/flash:1.2.11--hed695b0_5' }"
+        'https://depot.galaxyproject.org/singularity/flash:1.2.11--h5bf99c6_6' :
+        'biocontainers/flash:1.2.11--h5bf99c6_6' }"
 
     input:
     tuple val(meta), path(reads)
 
     output:
-    tuple val(meta), path("*.fastq.gz"), emit: reads
-    path "versions.yml"                , emit: versions
+    tuple val(meta), path("${prefix}.extendedFrags.fastq.gz"), emit: merged
+    tuple val(meta), path("${prefix}.notCombined_*.fastq.gz"), emit: notcombined
+    tuple val(meta), path("${prefix}.hist")                  , emit: histogram
+    path "versions.yml"                                      , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
 
     script:
     def args = task.ext.args ?: ''
-    def prefix = task.ext.prefix ?: "${meta.id}"
+    prefix = task.ext.prefix ?: "${meta.id}"
+    if ("$reads" == "${prefix}.extendedFrags.fastq.gz") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!"
+    if ("$reads" == "${prefix}.notCombined_1.fastq.gz") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!"
+    if ("$reads" == "${prefix}.notCombined_2.fastq.gz") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!"
+
     """
     flash \\
         $args \\
@@ -33,4 +39,17 @@ process FLASH {
         flash: \$(echo \$(flash --version 2>&1) | sed 's/^.*FLASH v//; s/ .*\$//')
     END_VERSIONS
     """
+
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+
+    touch ${prefix}.fastq.gz
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        flash: \$(echo \$(flash --version 2>&1) | sed 's/^.*FLASH v//; s/ .*\$//')
+    END_VERSIONS
+    """
 }
diff --git a/modules/nf-core/flash/meta.yml b/modules/nf-core/flash/meta.yml
@@ -28,10 +28,18 @@ output:
       description: |
         Groovy Map containing sample information
         e.g. [ id:'test', single_end:false ]
-  - reads:
+  - merged:
       type: file
       description: The merged fastq reads
-      pattern: "*fastq.gz"
+      pattern: ".extendedFrags.fastq.gz"
+  - notcombined:
+      type: file
+      description: Not combined reads from flash
+      pattern: ".notCombined_*.fastq.gz"
+  - histogram:
+      type: file
+      description: HistogramNumeric histogram of merged read lengths.
+      pattern: ".hist"
   - versions:
       type: file
       description: File containing software versions

diff --git a/modules/nf-core/flash/tests/main.nf.test b/modules/nf-core/flash/tests/main.nf.test
@@ -0,0 +1,37 @@
+nextflow_process {
+
+    name "Test Process FLASH"
+    script "../main.nf"
+    process "FLASH"
+    config "./nextflow.config"
+    tag "modules"
+    tag "modules_nfcore"
+    tag "flash"
+
+    test("sarscov2 - bam") {
+
+        when {
+            params{
+                outdir = "test"
+            }
+            process {
+                """
+                input[0] = [
+                    [ 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) ]
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+}
diff --git a/modules/nf-core/flash/tests/main.nf.test.snap b/modules/nf-core/flash/tests/main.nf.test.snap
@@ -0,0 +1,79 @@
+{
+    "sarscov2 - bam": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.extendedFrags.fastq.gz:md5,a2f163bfc21f9d6f9cb6b02c2bbcc57f"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        [
+                            "test.notCombined_1.fastq.gz:md5,3597e676a09cd3426ab3904a6ebed111",
+                            "test.notCombined_2.fastq.gz:md5,9bb71579b34567a15c11b30e46bae6aa"
+                        ]
+                    ]
+                ],
+                "2": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.hist:md5,6aa28c9bcb430ba16c0fd0115dacda5f"
+                    ]
+                ],
+                "3": [
+                    "versions.yml:md5,324e2f6592d7c6aa86f624076a88a10f"
+                ],
+                "histogram": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.hist:md5,6aa28c9bcb430ba16c0fd0115dacda5f"
+                    ]
+                ],
+                "merged": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.extendedFrags.fastq.gz:md5,a2f163bfc21f9d6f9cb6b02c2bbcc57f"
+                    ]
+                ],
+                "notcombined": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        [
+                            "test.notCombined_1.fastq.gz:md5,3597e676a09cd3426ab3904a6ebed111",
+                            "test.notCombined_2.fastq.gz:md5,9bb71579b34567a15c11b30e46bae6aa"
+                        ]
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,324e2f6592d7c6aa86f624076a88a10f"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-04-29T13:53:22.274475538"
+    }
+}
diff --git a/modules/nf-core/flash/tests/nextflow.config b/modules/nf-core/flash/tests/nextflow.config
@@ -0,0 +1,5 @@
+process {
+    withName: FLASH {
+        ext.args = '-m 20 -M 150'
+    }
+}
diff --git a/modules/nf-core/flash/tests/tags.yml b/modules/nf-core/flash/tests/tags.yml
@@ -0,0 +1,2 @@
+flash:
+  - "modules/nf-core/flash/**"
diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml
@@ -585,9 +585,6 @@ fgbio/sortbam:
 fgbio/zipperbams:
   - modules/nf-core/fgbio/zipperbams/**
   - tests/modules/nf-core/fgbio/zipperbams/**
-flash:
-  - modules/nf-core/flash/**
-  - tests/modules/nf-core/flash/**
 fqtk:
   - modules/nf-core/fqtk/**
   - modules/nf-core/untar/**

diff --git a/tests/modules/nf-core/flash/main.nf b/tests/modules/nf-core/flash/main.nf
diff --git a/tests/modules/nf-core/flash/nextflow.config b/tests/modules/nf-core/flash/nextflow.config
diff --git a/tests/modules/nf-core/flash/test.yml b/tests/modules/nf-core/flash/test.yml