Merge branch 'master' into update-bclconvert

nf-core · Nov 28, 2024 · 189973a · 189973a
2 parents a63933e + 61e2a51
commit 189973a
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diff --git a/modules/nf-core/gzrt/environment.yml b/modules/nf-core/gzrt/environment.yml
@@ -0,0 +1,6 @@
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - "bioconda::gzrt=0.8"
diff --git a/modules/nf-core/gzrt/main.nf b/modules/nf-core/gzrt/main.nf
@@ -0,0 +1,53 @@
+process GZRT {
+    tag "$meta.id"
+    label 'process_single'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/gzrt:0.8--he4a0461_0':
+        'biocontainers/gzrt:0.8--he4a0461_0' }"
+
+    input:
+    tuple val(meta), path(fastqgz)
+
+    output:
+    tuple val(meta), path("*_recovered.fastq.gz"), emit: fastqrecovered
+    path "versions.yml"                          , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    if (fastqgz.extension != "gz") {
+        error "GZRT works with .gz files only."
+    }
+
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    mkfifo temp_recovered.fastq
+    gzrecover -o temp_recovered.fastq ${fastqgz} &
+    gzip < temp_recovered.fastq > ${prefix}_recovered.fastq.gz
+    rm temp_recovered.fastq
+
+    soft_line="${task.process}"
+    ver_line="gzrt: \$(gzrecover -V |& sed '1!d ; s/gzrecover //')"
+    cat <<-END_VERSIONS > versions.yml
+    "\${soft_line}":
+        \${ver_line}
+    END_VERSIONS
+    """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    echo "gzrt module" > ${prefix}_recovered.fastq && gzip ${prefix}_recovered.fastq
+
+    soft_line="${task.process}"
+    ver_line="gzrt: \$(gzrecover -V |& sed '1!d ; s/gzrecover //')"
+
+    cat <<-END_VERSIONS > versions.yml
+    "\${soft_line}":
+        \${ver_line}
+    END_VERSIONS
+    """
+}
diff --git a/modules/nf-core/gzrt/meta.yml b/modules/nf-core/gzrt/meta.yml
@@ -0,0 +1,55 @@
+name: "gzrt"
+description: gzrecover is a program that will attempt to extract any readable data out of a gzip file that has been corrupted
+keywords:
+  - corrupted
+  - fastq
+  - recovery
+tools:
+  - "gzrt":
+      description: "Unofficial build of the gzip Recovery Toolkit aka gzrecover"
+      homepage: "https://www.urbanophile.com/arenn/hacking/gzrt/gzrt.html"
+      documentation: "https://www.urbanophile.com/arenn/hacking/gzrt/gzrt.html"
+      tool_dev_url: "https://github.com/arenn/gzrt"
+      doi: "no DOI available"
+      licence: ["GPL v2"]
+      identifier: ""
+
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. `[ id:'sample1', single_end:false ]`
+
+    - fastqgz:
+        type: file
+        description: FASTQ.gz file
+        pattern: "*.{gz}"
+        ontologies:
+          - edam: "http://edamontology.org/format_3989"
+
+output:
+  - fastqrecovered:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'sample1', single_end:false ]`
+      - "*_recovered.fastq.gz":
+          type: file
+          description: Recovered FASTQ.gz file
+          pattern: "*.{gz}"
+          ontologies:
+            - edam: "http://edamontology.org/format_3989"
+
+  - versions:
+      - "versions.yml":
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
+
+authors:
+  - "@mazzalab"
+maintainers:
+  - "@mazzalab"
+  - "@tm4zza"
diff --git a/modules/nf-core/gzrt/tests/main.nf.test b/modules/nf-core/gzrt/tests/main.nf.test
@@ -0,0 +1,55 @@
+nextflow_process {
+
+    name "Test Process GZRT"
+    script "../main.nf"
+    process "GZRT"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "gzrt"
+
+    test("Run gzrt on 30 paired-end reads - fastq.gz") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    file('https://raw.githubusercontent.com/nf-core/test-datasets/fastqrepair/testdata/test_30reads_R1.fastq.gz', checkIfExists: true),
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+    test("Run gzrt on 30 paired-end reads - fastq.gz - stub") {
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    file('https://raw.githubusercontent.com/nf-core/test-datasets/fastqrepair/testdata/test_30reads_R1.fastq.gz', checkIfExists: true),
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+}
diff --git a/modules/nf-core/gzrt/tests/main.nf.test.snap b/modules/nf-core/gzrt/tests/main.nf.test.snap
@@ -0,0 +1,72 @@
+{
+    "Run gzrt on 30 paired-end reads - fastq.gz": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test_recovered.fastq.gz:md5,5eca10f954656478b5af96868222eec4"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,b9467d4cb860eb2941a2078a3dd3cf41"
+                ],
+                "fastqrecovered": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test_recovered.fastq.gz:md5,5eca10f954656478b5af96868222eec4"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,b9467d4cb860eb2941a2078a3dd3cf41"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.1"
+        },
+        "timestamp": "2024-11-27T20:04:34.442659"
+    },
+    "Run gzrt on 30 paired-end reads - fastq.gz - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test_recovered.fastq.gz:md5,0f8202ea19c8ce3f69f4413bf139b29c"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,b9467d4cb860eb2941a2078a3dd3cf41"
+                ],
+                "fastqrecovered": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test_recovered.fastq.gz:md5,0f8202ea19c8ce3f69f4413bf139b29c"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,b9467d4cb860eb2941a2078a3dd3cf41"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.1"
+        },
+        "timestamp": "2024-11-27T20:04:46.182206"
+    }
+}
diff --git a/modules/nf-core/hifiasm/environment.yml b/modules/nf-core/hifiasm/environment.yml
@@ -2,4 +2,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::hifiasm=0.20.0
+  - bioconda::hifiasm=0.21.0
diff --git a/modules/nf-core/hifiasm/main.nf b/modules/nf-core/hifiasm/main.nf
@@ -4,8 +4,8 @@ process HIFIASM {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/hifiasm:0.20.0--h43eeafb_0' :
-        'biocontainers/hifiasm:0.20.0--h43eeafb_0' }"
+        'https://depot.galaxyproject.org/singularity/hifiasm:0.21.0--h43eeafb_0' :
+        'biocontainers/hifiasm:0.21.0--h43eeafb_0' }"
 
     input:
     tuple val(meta) , path(reads)

diff --git a/modules/nf-core/hifiasm/tests/main.nf.test.snap b/modules/nf-core/hifiasm/tests/main.nf.test.snap
@@ -42,14 +42,14 @@
                 ]
             ],
             [
-                "versions.yml:md5,6a23f7ea8bae71905c537cd521cffcb8"
+                "versions.yml:md5,4c02458be007ef6776c2991fbb13f879"
             ]
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.1"
         },
-        "timestamp": "2024-10-23T14:01:04.528764919"
+        "timestamp": "2024-11-28T10:51:30.175326435"
     },
     "homo_sapiens pacbio hifi [fastq, [,], [fastq, fastq] ]": {
         "content": [
@@ -78,14 +78,14 @@
                 ]
             ],
             [
-                "versions.yml:md5,6a23f7ea8bae71905c537cd521cffcb8"
+                "versions.yml:md5,4c02458be007ef6776c2991fbb13f879"
             ]
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.1"
         },
-        "timestamp": "2024-10-23T14:08:48.081396092"
+        "timestamp": "2024-11-28T10:52:15.111066189"
     },
     "homo_sapiens pacbio hifi [fastq, [,], [,] ] - stub": {
         "content": [
@@ -115,7 +115,7 @@
                     ]
                 ],
                 "11": [
-                    "versions.yml:md5,6a23f7ea8bae71905c537cd521cffcb8"
+                    "versions.yml:md5,4c02458be007ef6776c2991fbb13f879"
                 ],
                 "2": [
                     [
@@ -270,15 +270,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,6a23f7ea8bae71905c537cd521cffcb8"
+                    "versions.yml:md5,4c02458be007ef6776c2991fbb13f879"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.1"
         },
-        "timestamp": "2024-10-23T14:09:13.475508542"
+        "timestamp": "2024-11-28T10:53:06.003871811"
     },
     "homo_sapiens pacbio hifi [fastq, [yak, yak], [,] ]": {
         "content": [
@@ -307,13 +307,13 @@
                 ]
             ],
             [
-                "versions.yml:md5,6a23f7ea8bae71905c537cd521cffcb8"
+                "versions.yml:md5,4c02458be007ef6776c2991fbb13f879"
             ]
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.1"
         },
-        "timestamp": "2024-10-23T13:33:47.765243676"
+        "timestamp": "2024-11-28T10:51:45.301359171"
     }
 }
diff --git a/modules/nf-core/mafft/guidetree/meta.yml b/modules/nf-core/mafft/guidetree/meta.yml
@@ -44,4 +44,3 @@ authors:
   - "@luisas"
 maintainers:
   - "@luisas"
-
diff --git a/modules/nf-core/mgikit/demultiplex/environment.yml b/modules/nf-core/mgikit/demultiplex/environment.yml
@@ -0,0 +1,5 @@
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - bioconda::mgikit=0.1.6