Merge branch 'master' into regressive

modules/nf-core/elprep/fastatoelfasta/environment.yml

@@ -0,0 +1,7 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - "bioconda::elprep=5.1.3"

modules/nf-core/elprep/fastatoelfasta/main.nf

@@ -0,0 +1,50 @@
+process ELPREP_FASTATOELFASTA {
+    tag "$meta.id"
+    label 'process_low'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/elprep:5.1.3--he881be0_1':
+        'biocontainers/elprep:5.1.3--he881be0_1' }"
+
+    input:
+    tuple val(meta), path(fasta)
+
+    output:
+    tuple val(meta), path("*.elfasta")          , emit: elfasta
+    tuple val(meta), path("logs/elprep/elprep*"), emit: log
+    path "versions.yml"                         , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    elprep fasta-to-elfasta \\
+        $fasta \\
+        ${prefix}.elfasta \\
+        --log-path ./
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        elprep: \$(elprep 2>&1 | head -n2 | tail -n1 |sed 's/^.*version //;s/ compiled.*\$//')
+    END_VERSIONS
+    """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def timestamp = "${java.time.OffsetDateTime.now().format(java.time.format.DateTimeFormatter.ISO_DATE_TIME)}"
+
+    """
+    mkdir -p logs/elprep
+
+    touch ${prefix}.elfasta
+    touch logs/elprep/elprep-${timestamp}.log
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        elprep: \$(elprep 2>&1 | head -n2 | tail -n1 |sed 's/^.*version //;s/ compiled.*\$//')
+    END_VERSIONS
+    """
+}

modules/nf-core/elprep/fastatoelfasta/meta.yml

@@ -0,0 +1,55 @@
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
+name: "elprep_fastatoelfasta"
+description: Convert a file in FASTA format to the ELFASTA format
+keywords:
+  - fasta
+  - elfasta
+  - elprep
+tools:
+  - "elprep":
+      description: "elPrep is a high-performance tool for preparing .sam/.bam files
+        for variant calling in sequencing pipelines. It can be used as a drop-in replacement
+        for SAMtools/Picard/GATK4."
+      homepage: "https://github.com/ExaScience/elprep"
+      documentation: "https://github.com/ExaScience/elprep"
+      tool_dev_url: "https://github.com/ExaScience/elprep"
+      doi: "10.1371/journal.pone.0244471"
+      licence: ["AGPL v3"]
+      identifier: biotools:elprep
+
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. `[ id:'sample1', single_end:false ]`
+    - fasta:
+        type: file
+        description: FASTA file
+        pattern: "*.{fasta,fa,fna}"
+output:
+  - elfasta:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'sample1', single_end:false ]`
+          pattern: "*.elfasta"
+      - "*.elfasta":
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'sample1', single_end:false ]`
+          pattern: "*.elfasta"
+  - log:
+      - meta: {}
+      - logs/elprep/elprep*: {}
+  - versions:
+      - versions.yml:
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
+authors:
+  - "@nvnieuwk"
+maintainers:
+  - "@nvnieuwk"

modules/nf-core/elprep/fastatoelfasta/tests/main.nf.test

@@ -0,0 +1,66 @@
+nextflow_process {
+
+    name "Test Process ELPREP_FASTATOELFASTA"
+    script "../main.nf"
+    process "ELPREP_FASTATOELFASTA"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "elprep"
+    tag "elprep/fastatoelfasta"
+
+    test("sarscov2 - fasta") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true),
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    process.out.elfasta,
+                    process.out.log.collect { [it[0], file(it[1]).exists()] },
+                    process.out.versions
+                ).match() }
+            )
+        }
+
+    }
+
+    test("sarscov2 - fasta - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true),
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    process.out.elfasta,
+                    process.out.log.collect { [it[0], file(it[1]).exists()] },
+                    process.out.versions
+                ).match() }
+            )
+        }
+
+    }
+
+}

modules/nf-core/elprep/fastatoelfasta/tests/main.nf.test.snap

@@ -0,0 +1,62 @@
+{
+    "sarscov2 - fasta - stub": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.elfasta:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    true
+                ]
+            ],
+            [
+                "versions.yml:md5,bf313ed1289a8969464c5593b0ff67be"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-10-18T14:29:50.861439255"
+    },
+    "sarscov2 - fasta": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.elfasta:md5,09a6f76bed84ee211ef0d962e26c77f1"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    true
+                ]
+            ],
+            [
+                "versions.yml:md5,bf313ed1289a8969464c5593b0ff67be"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-10-18T14:25:24.238816922"
+    }
+}

modules/nf-core/pangolin/environment.yml

@@ -2,4 +2,6 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::pangolin=4.2
+  - bioconda::pangolin-data=1.30
+  - bioconda::pangolin=4.3
+  - bioconda::snakemake=7.30.1

modules/nf-core/pangolin/main.nf

@@ -4,8 +4,8 @@ process PANGOLIN {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/pangolin:4.2--pyhdfd78af_1' :
-        'biocontainers/pangolin:4.2--pyhdfd78af_1' }"
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/bb/bb7bac48e43a9cd6274e1f99c761a5785b74f6d8a55313ee634aaffbe87c1869/data' :
+        'community.wave.seqera.io/library/pangolin-data_pangolin_snakemake:5bbc297f7502ff33' }"
 
     input:
     tuple val(meta), path(fasta)
@@ -21,6 +21,8 @@ process PANGOLIN {
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
+    export XDG_CACHE_HOME=/tmp/.cache
+
     pangolin \\
         $fasta\\
         --outfile ${prefix}.pangolin.csv \\

modules/nf-core/pangolin/meta.yml

@@ -5,7 +5,7 @@ keywords:
   - pangolin
   - lineage
 tools:
-  - star:
+  - pangolin:
       description: |
         Phylogenetic Assignment of Named Global Outbreak LINeages
       homepage: https://github.com/cov-lineages/pangolin#pangolearn-description
@@ -24,9 +24,9 @@ input:
 output:
   - report:
       - meta:
-          type: file
-          description: Pangolin lineage report
-          pattern: "*.{csv}"
+          type: map
+          description: |
+            Groovy Map containing sample information
       - "*.csv":
           type: file
           description: Pangolin lineage report

modules/nf-core/pangolin/tests/main.nf.test

@@ -0,0 +1,57 @@
+nextflow_process {
+
+    name "Test Process PANGOLIN"
+    script "../main.nf"
+    process "PANGOLIN"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "pangolin"
+
+    test("sarscov2 genome [fasta]") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                            [ id:'test' ], // meta map
+                            [ file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ]
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+    test("sarscov2 genome [fasta] - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                            [ id:'test' ], // meta map
+                            [ file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ]
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+}