Add nf-test to porechop_abi (#6049)

* Add nf-test to the module porechop_abi * update standard output * update licence * update tags.yml * Update modules/nf-core/porechop/abi/main.nf Co-authored-by: Simon Pearce <[email protected]> * Update modules/nf-core/porechop/abi/main.nf Co-authored-by: Simon Pearce <[email protected]> * Update modules/nf-core/porechop/abi/main.nf Co-authored-by: Simon Pearce <[email protected]> * Update modules/nf-core/porechop/abi/meta.yml Co-authored-by: Simon Pearce <[email protected]> * remove pytest and update the prefix * Update modules/nf-core/porechop/abi/main.nf Co-authored-by: Simon Pearce <[email protected]> * Update modules/nf-core/porechop/abi/tests/main.nf.test Co-authored-by: Simon Pearce <[email protected]> * Update modules/nf-core/porechop/abi/tests/main.nf.test Co-authored-by: Simon Pearce <[email protected]> * Update modules/nf-core/porechop/abi/tests/main.nf.test Co-authored-by: Simon Pearce <[email protected]> * update main.nf.test * Update main.nf check input and output are not same --------- Co-authored-by: Simon Pearce <[email protected]>
nf-core · Jul 30, 2024 · 870f9af · 870f9af
1 parent e61e5a1
commit 870f9af
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Showing 7 changed files with 180 additions and 10 deletions.
diff --git a/modules/nf-core/porechop/abi/environment.yml b/modules/nf-core/porechop/abi/environment.yml
@@ -1,3 +1,5 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
 name: porechop_abi
 channels:
   - conda-forge

diff --git a/modules/nf-core/porechop/abi/main.nf b/modules/nf-core/porechop/abi/main.nf
@@ -11,23 +11,37 @@ process PORECHOP_ABI {
     tuple val(meta), path(reads)
 
     output:
-    tuple val(meta), path("*.fastq.gz"), emit: reads
-    tuple val(meta), path("*.log")     , emit: log
-    path "versions.yml"                , emit: versions
+    tuple val(meta), path("*.fastq.gz") , emit: reads
+    tuple val(meta), path("*.log")      , emit: log
+    path "versions.yml"                 , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
 
     script:
     def args = task.ext.args ?: ''
-    def prefix = task.ext.prefix ?: "${meta.id}"
+    def prefix = task.ext.prefix ?: "${meta.id}.porechop_abi"
+    if ("$reads" == "${prefix}.fastq.gz") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!"
     """
     porechop_abi \\
         --input $reads \\
         --threads $task.cpus \\
         $args \\
         --output ${prefix}.fastq.gz \\
-        > ${prefix}.log
+        | tee ${prefix}.log
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        porechop_abi: \$( porechop_abi --version )
+    END_VERSIONS
+    """
+
+    stub:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}.porechop_abi"
+    """
+    echo "" | gzip > ${prefix}.fastq.gz
+    touch ${prefix}.log
+
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         porechop_abi: \$( porechop_abi --version )

diff --git a/modules/nf-core/porechop/abi/meta.yml b/modules/nf-core/porechop/abi/meta.yml
@@ -11,7 +11,7 @@ tools:
       documentation: "https://github.com/bonsai-team/Porechop_ABI"
       tool_dev_url: "https://github.com/bonsai-team/Porechop_ABI"
       doi: "10.1101/2022.07.07.499093"
-      licence: "['GPL v3']"
+      licence: ["MIT"]
 input:
   - meta:
       type: map
@@ -35,12 +35,14 @@ output:
   - reads:
       type: file
       description: Adapter-trimmed fastq.gz file
-      pattern: "*fastq.gz"
+      pattern: "*.fastq.gz"
   - log:
       type: file
       description: Log file containing stdout information
       pattern: "*.log"
 authors:
   - "@sofstam"
+  - "LilyAnderssonLee"
 maintainers:
   - "@sofstam"
+  - "LilyAnderssonLee"
diff --git a/modules/nf-core/porechop/abi/tests/main.nf.test b/modules/nf-core/porechop/abi/tests/main.nf.test
@@ -0,0 +1,59 @@
+nextflow_process {
+
+    name "Test Process PORECHOP_ABI"
+    script "../main.nf"
+    process "PORECHOP_ABI"
+    tag "modules"
+    tag "modules_nfcore"
+    tag "porechop"
+    tag "porechop/abi"
+
+    test("sarscov2-nanopore") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test'], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/nanopore/fastq/test.fastq.gz', checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    process.out.reads,
+                    file(process.out.log.get(0).get(1)).readLines()[20..40],
+                    process.out.versions).match()
+                }
+            )
+        }
+    }
+
+    test("sarscov2-nanopore - stub") {
+
+        options "-stub"
+
+        when {
+
+            process {
+                """
+                input[0] = [
+                    [ id:'test'], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/nanopore/fastq/test.fastq.gz', checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+}
diff --git a/modules/nf-core/porechop/abi/tests/main.nf.test.snap b/modules/nf-core/porechop/abi/tests/main.nf.test.snap
@@ -0,0 +1,94 @@
+{
+    "sarscov2-nanopore": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.porechop_abi.fastq.gz:md5,886fdb859fb50e0dddd35007bcff043e"
+                ]
+            ],
+            [
+                "                                        Best               \u001b[0m",
+                "                                        read       Best    \u001b[0m",
+                "                                        start      read end\u001b[0m",
+                "  \u001b[4mSet                                   %ID        %ID     \u001b[0m",
+                "  \u001b[32mSQK-NSK007                               100.0       73.1\u001b[0m",
+                "  Rapid                                     40.4        0.0",
+                "  RBK004_upstream                           77.5        0.0",
+                "  SQK-MAP006                                75.8       72.7",
+                "  SQK-MAP006 short                          65.5       66.7",
+                "  PCR adapters 1                            73.9       69.6",
+                "  PCR adapters 2                            80.0       72.7",
+                "  PCR adapters 3                            70.8       69.6",
+                "  1D^2 part 1                               71.4       70.0",
+                "  1D^2 part 2                               84.8       75.8",
+                "  cDNA SSP                                  63.0       61.7",
+                "  \u001b[32mBarcode 1 (reverse)                      100.0      100.0\u001b[0m",
+                "  Barcode 2 (reverse)                       70.8       69.2",
+                "  Barcode 3 (reverse)                       76.0       70.4",
+                "  Barcode 4 (reverse)                       74.1       71.4",
+                "  Barcode 5 (reverse)                       77.8       80.8",
+                "  Barcode 6 (reverse)                       73.1       70.8"
+            ],
+            [
+                "versions.yml:md5,0e9e5e0d35a68ff8e6490c949b257f98"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.04.1"
+        },
+        "timestamp": "2024-07-29T13:50:49.318599"
+    },
+    "sarscov2-nanopore - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.porechop_abi.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.porechop_abi.log:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,0e9e5e0d35a68ff8e6490c949b257f98"
+                ],
+                "log": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.porechop_abi.log:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "reads": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.porechop_abi.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,0e9e5e0d35a68ff8e6490c949b257f98"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.04.1"
+        },
+        "timestamp": "2024-07-29T13:50:54.425389"
+    }
+}
diff --git a/modules/nf-core/porechop/abi/tests/tags.yml b/modules/nf-core/porechop/abi/tests/tags.yml
@@ -0,0 +1,2 @@
+porechop/abi:
+  - "modules/nf-core/porechop/abi/**"
diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml
@@ -1229,9 +1229,6 @@ pmdtools/filter:
 pneumocat:
   - modules/nf-core/pneumocat/**
   - tests/modules/nf-core/pneumocat/**
-porechop/abi:
-  - modules/nf-core/porechop/abi/**
-  - tests/modules/nf-core/porechop/abi/**
 preseq/ccurve:
   - modules/nf-core/preseq/ccurve/**
   - tests/modules/nf-core/preseq/ccurve/**