bcftools csq (#6605)

* bcftools csq

* fix lint / format

* env.yml

* move fun at bottom

* Update modules/nf-core/bcftools/csq/main.nf

Co-authored-by: Sateesh_Peri <[email protected]>

---------

Co-authored-by: Sateesh_Peri <[email protected]>

modules/nf-core/bcftools/csq/environment.yml

@@ -0,0 +1,5 @@
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - "bioconda::bcftools=1.20"

modules/nf-core/bcftools/csq/main.nf

@@ -0,0 +1,81 @@
+
+process BCFTOOLS_CSQ {
+    tag "$meta.id"
+    label 'process_single'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/bcftools:1.20--h8b25389_1':
+        'biocontainers/bcftools:1.20--h8b25389_1' }"
+
+
+    input:
+    tuple val(meta), path(vcf)
+    tuple val(meta2), path(fasta)
+    tuple val(meta3), path(fai)
+    tuple val(meta4), path(gff3)
+
+    output:
+    tuple val(meta), path("*.${extension}"), emit: vcf
+    tuple val(meta), path("*.tbi")         , emit: tbi, optional: true
+    tuple val(meta), path("*.csi")         , emit: csi, optional: true
+    path  "versions.yml"                   , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+
+    extension = getVcfExtension(args);
+
+    if ("$vcf" == "${prefix}.${extension}") error "Input and output names are the same, set prefix in module configuration to disambiguate!"
+
+    """
+    bcftools csq \\
+        --output ${prefix}.${extension} \\
+        --threads ${task.cpus} \\
+        --fasta-ref ${fasta} \\
+        --gff-annot ${gff3} \\
+        $args \\
+        $vcf
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        bcftools: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//')
+    END_VERSIONS
+    """
+
+    stub:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    extension = getVcfExtension(args);
+
+    def index = args.contains("--write-index=tbi") || args.contains("-W=tbi") ? "tbi" :
+                args.contains("--write-index=csi") || args.contains("-W=csi") ? "csi" :
+                args.contains("--write-index") || args.contains("-W") ? "csi" :
+                ""
+    def create_cmd = extension.endsWith(".gz") ? "echo '' | gzip >" : "touch"
+    def create_index = extension.endsWith(".gz") && index.matches("csi|tbi") ? "touch ${prefix}.${extension}.${index}" : ""
+
+    if ("$vcf" == "${prefix}.${extension}") error "Input and output names are the same, set prefix in module configuration to disambiguate!"
+
+    """
+    ${create_cmd} ${prefix}.${extension}
+    ${create_index}
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        bcftools: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//')
+    END_VERSIONS
+    """
+}
+// Custom Functions
+String getVcfExtension(String args) {
+    return args.contains("--output-type b") || args.contains("-Ob") ? "bcf.gz" :
+        args.contains("--output-type u") || args.contains("-Ou") ? "bcf" :
+        args.contains("--output-type z") || args.contains("-Oz") ? "vcf.gz" :
+        args.contains("--output-type v") || args.contains("-Ov") ? "vcf" :
+        "vcf";
+}

modules/nf-core/bcftools/csq/meta.yml

@@ -0,0 +1,81 @@
+name: bcftools_csq
+description: bcftools Haplotype-aware consequence caller
+keywords:
+  - annotation
+  - gff
+  - gff3
+  - protein
+  - functional
+  - vcf
+  - bcf
+  - bcftools
+tools:
+  - reheader:
+      description: |
+        Haplotype-aware consequence caller
+      homepage: http://samtools.github.io/bcftools/bcftools.html
+      documentation: http://samtools.github.io/bcftools/bcftools.html#csq
+      doi: 10.1093/gigascience/giab008
+      licence: ["MIT"]
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - vcf:
+      type: file
+      description: VCF/BCF file
+      pattern: "*.{vcf.gz,vcf,bcf}"
+  - meta2:
+      type: map
+      description: |
+        Groovy Map containing fasta information
+  - fasta:
+      type: file
+      description: Fasta reference
+      pattern: "*.{fasta,fa}"
+  - meta3:
+      type: map
+      description: |
+        Groovy Map containing fai information
+  - fai:
+      type: file
+      description: Fasta index
+      pattern: "*.{fai}"
+  - meta4:
+      type: map
+      description: |
+        Groovy Map containing gff3 information
+  - gff3:
+      type: file
+      description: GFF3 file
+      pattern: "*.{gff,gff.gz,gff3,gff3.gz}"
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - vcf:
+      type: file
+      description: VCF with annotation, bgzipped per default
+      pattern: "*.{vcf,vcf.gz,bcf,bcf.gz}"
+  - tbi:
+      type: file
+      description: Alternative VCF file index
+      pattern: "*.tbi"
+  - csi:
+      type: file
+      description: Default VCF file index
+      pattern: "*.csi"
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+
+authors:
+  - "@lindenb"
+
+maintainers:
+  - "@lindenb"

modules/nf-core/bcftools/csq/tests/main.nf.test

@@ -0,0 +1,51 @@
+nextflow_process {
+
+    name "Test Process BCFTOOLS_CSQ"
+    script "../main.nf"
+    process "BCFTOOLS_CSQ"
+    tag "modules"
+    tag "modules_nfcore"
+    tag "bcftools"
+    tag "bcftools/csq"
+
+    test("homo_sapiens") {
+
+        config "./vcf.config"
+        when {
+
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/germlineresources/dbsnp_138.hg38.vcf.gz', checkIfExists: true)
+                ]
+                input[1] = [
+                    [ : ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta', checkIfExists: true)
+                ]
+                input[2] = [
+                    [ : ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai', checkIfExists: true)
+                ]
+                input[3] = [
+                    [ : ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gff3', checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                                path(process.out.vcf[0][1]).vcf.variantsMD5,
+                                process.out.versions
+                                ).match()
+                }
+            )
+        }
+
+    }
+
+}

modules/nf-core/bcftools/csq/tests/main.nf.test.snap

@@ -0,0 +1,15 @@
+{
+    "homo_sapiens": {
+        "content": [
+            "807319f441f639c33708781757da53ee",
+           [
+           "versions.yml:md5,13a1a38a47f60c47fd15a32552492bbf"
+           ]
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-09-06T16:02:00.380988135"
+    }
+}

modules/nf-core/bcftools/csq/tests/tags.yml

@@ -0,0 +1,2 @@
+bcftools/csq:
+  - "modules/nf-core/bcftools/csq/**"

modules/nf-core/bcftools/csq/tests/vcf.config

@@ -0,0 +1,4 @@
+process {
+    ext.args = { "--local-csq --ncsq 20 --unify-chr-names 1 -Ov " }
+    ext.prefix = "tested"
+}