Merge branch 'master' into fix-mmseqs-compressed

.github/workflows/lint.yml

@@ -93,7 +93,7 @@ jobs:
           echo ${{ steps.module_names.outputs.result }}
 
   nf-core-lint-modules:
-    runs-on: ${{ github.event.inputs.runners  || 'self-hosted' }}
+    runs-on: ${{ github.event.inputs.runners  || 'ubuntu-latest' }}
     name: nf-core lint modules
     needs: nf-core-changes
     if: ${{ (needs.nf-core-changes.outputs.modules == 'true') }}

.github/workflows/nf-test.yml

@@ -75,7 +75,7 @@ jobs:
           echo ${{ steps.outputs.outputs.modules }}
           echo ${{ steps.outputs.outputs.subworkflows }}
   nf-test:
-    runs-on: ${{ github.event.inputs.runners || 'self-hosted' }}
+    runs-on: ${{ github.event.inputs.runners || 'ubuntu-latest' }}
     name: "Test | ${{ matrix.profile }} | ${{ matrix.shard }}"
     needs: nf-test-changes
     if: ${{ needs.nf-test-changes.outputs.modules != '[]' || needs.nf-test-changes.outputs.subworkflows != '[]' }}

.github/workflows/pytest-workflow.yml

@@ -62,7 +62,7 @@ jobs:
           echo ${{ steps.tags.outputs.subworkflows }}
 
   pytest:
-    runs-on: ${{ github.event.inputs.runners  || 'self-hosted' }}
+    runs-on: ${{ github.event.inputs.runners  || 'ubuntu-latest' }}
     name: pytest
     needs: [pytest-changes]
     if: needs.pytest-changes.outputs.tags != '[]'

modules/nf-core/agat/convertbed2gff/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::agat=1.4.2"

modules/nf-core/agat/convertbed2gff/main.nf

@@ -0,0 +1,45 @@
+process AGAT_CONVERTBED2GFF {
+    tag "$meta.id"
+    label 'process_single'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/agat:1.4.2--pl5321hdfd78af_0' :
+        'biocontainers/agat:1.4.2--pl5321hdfd78af_0' }"
+
+    input:
+    tuple val(meta), path(bed)
+
+    output:
+    tuple val(meta), path("*.gff")  , emit: gff
+    path "versions.yml"             , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    agat_convert_bed2gff.pl \\
+        --bed $bed \\
+        --output ${prefix}.gff \\
+        $args
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        agat: \$(agat_convert_bed2gff.pl --help | sed -n 's/.*(AGAT) - Version: \\(.*\\) .*/\\1/p')
+    END_VERSIONS
+    """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.gff
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        agat: \$(agat_convert_bed2gff.pl --help | sed -n 's/.*(AGAT) - Version: \\(.*\\) .*/\\1/p')
+    END_VERSIONS
+    """
+}

modules/nf-core/agat/convertbed2gff/meta.yml

@@ -0,0 +1,49 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
+name: agat_convertbed2gff
+description: |
+  Takes a bed12 file and converts to a GFF3 file
+keywords:
+  - genome
+  - bed
+  - gff
+  - conversion
+tools:
+  - agat:
+      description: "AGAT is a toolkit for manipulation and getting information from
+        GFF/GTF files"
+      homepage: "https://github.com/NBISweden/AGAT"
+      documentation: "https://agat.readthedocs.io/"
+      tool_dev_url: "https://github.com/NBISweden/AGAT"
+      doi: "10.5281/zenodo.3552717"
+      licence: ["GPL v3"]
+      identifier: biotools:AGAT
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test', single_end:false ]
+    - bed:
+        type: file
+        description: Input bed12 file
+        pattern: "*.bed"
+output:
+  - gff:
+      - meta:
+          type: map
+          description: Groovy Map containing sample information
+      - "*.gff":
+          type: file
+          description: Output GFF3 file
+          pattern: "*.{gff}"
+  - versions:
+      - versions.yml:
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
+
+authors:
+  - "@GallVp"
+maintainers:
+  - "@GallVp"

modules/nf-core/agat/convertbed2gff/tests/main.nf.test

@@ -0,0 +1,58 @@
+nextflow_process {
+
+    name "Test Process AGAT_CONVERTBED2GFF"
+    script "../main.nf"
+    process "AGAT_CONVERTBED2GFF"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "agat"
+    tag "agat/convertbed2gff"
+
+    test("sarscov2 - bed12") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed12', checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+    test("sarscov2 - bam - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed12', checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+}

modules/nf-core/agat/convertbed2gff/tests/main.nf.test.snap

@@ -0,0 +1,70 @@
+{
+    "sarscov2 - bam - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.gff:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,ccfb13a5b261f660922e1ed845e68cbc"
+                ],
+                "gff": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.gff:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,ccfb13a5b261f660922e1ed845e68cbc"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.10.3"
+        },
+        "timestamp": "2025-01-15T14:02:09.48826"
+    },
+    "sarscov2 - bed12": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.gff:md5,4e5a23a6babac6d5b1bcfa06c5b12518"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,ccfb13a5b261f660922e1ed845e68cbc"
+                ],
+                "gff": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.gff:md5,4e5a23a6babac6d5b1bcfa06c5b12518"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,ccfb13a5b261f660922e1ed845e68cbc"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.10.3"
+        },
+        "timestamp": "2025-01-15T14:02:03.549345"
+    }
+}

modules/nf-core/immunedeconv/environment.yml

@@ -0,0 +1,5 @@
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - bioconda::r-immunedeconv=2.1.2

modules/nf-core/immunedeconv/main.nf

@@ -0,0 +1,37 @@
+process IMMUNEDECONV {
+    tag "$meta.id"
+    label 'process_single'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+    'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/22/22cb85f1b69ceff45b83e0fdb7b96d9ae29c8aafeaa0707d64cc4628982977ab/data' :
+    'community.wave.seqera.io/library/r-immunedeconv:2.1.2--e1bb1ea1cf505cb3' }"
+
+    input:
+    tuple val(meta), path(input_file), val(method), val(function)
+    val gene_symbol_col
+
+    output:
+    tuple val(meta), path("*.deconvolution_results.tsv"), emit: deconv_table
+    tuple val(meta), path("*.png"),                       emit: deconv_plots, optional: true
+    path "versions.yml",                                  emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    template 'immunedeconv.R'
+
+    stub:
+    prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.deconvolution_results.tsv
+    touch ${prefix}.plot1_stacked_bar_chart.png
+    touch ${prefix}.plot2_points_with_facets.png
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        r-immunedeconv: \$(Rscript -e "cat(as.character(packageVersion('immunedeconv')))")
+    END_VERSIONS
+    """
+}

modules/nf-core/immunedeconv/meta.yml

@@ -0,0 +1,67 @@
+name: immunedeconv
+description: Perform immune cell deconvolution using RNA-seq data and various computational methods.
+keywords:
+  - Immune Deconvolution
+  - RNA-seq
+  - Bioinformatics Tools
+  - Computational Immunology
+tools:
+  - immunedeconv:
+      description: |
+        The immunedeconv R package provides functions for immune cell deconvolution
+        from RNA-seq data. It supports multiple deconvolution methods and generates
+        results as well as visualizations.
+      homepage: https://github.com/icbi-lab/immunedeconv
+      documentation: https://icbi-lab.github.io/immunedeconv/
+      licence: ["GPL-2"]
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. `[ id:'sample1', single_end:false ]`
+    - input_file:
+        type: file
+        description: Input matrix with genes in rows and samples in columns.
+        pattern: "*.tsv"
+    - method:
+        type: string
+        description: The deconvolution method to use (e.g., 'CIBERSORT', 'EPIC', 'xCell').
+    - function:
+        type: string
+        description: The specific function from immunedeconv to execute for analysis.
+  - - gene_symbol_col:
+        type: string
+        description: Column name for gene symbols in the matrix input file.
+output:
+  - deconv_table:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'sample1', single_end:false ]`
+      - "*.deconvolution_results.tsv":
+          type: file
+          description: Results table containing deconvolution data.
+          pattern: "*.deconvolution_results.tsv"
+  - deconv_plots:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'sample1', single_end:false ]`
+      - "*.png":
+          type: file
+          description: Visualization plots generated during deconvolution.
+          pattern: "*.png"
+  - versions:
+      - versions.yml:
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
+authors:
+  - "@grst"
+  - "@nschcolnicov"
+maintainers:
+  - "@grst"
+  - "@nschcolnicov"