Igv reports (nf-core#5263)

* add inital igvreports module

* add full input and tests

---------

Co-authored-by: Andrea Telatin <15690844+telatin@users.noreply.github.com>

modules/nf-core/igvreports/environment.yml

@@ -0,0 +1,9 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+name: "igvreports"
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - "bioconda::igv-reports=1.12.0"

modules/nf-core/igvreports/main.nf

@@ -0,0 +1,48 @@
+process IGVREPORTS {
+    tag "$meta.id"
+    label 'process_low'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/igv-reports:1.12.0--pyh7cba7a3_0':
+        'biocontainers/igv-reports:1.12.0--pyh7cba7a3_0' }"
+
+    input:
+    tuple val(meta), path(sites)
+    path genomeFasta //optional genome fasta file
+
+    output:
+    tuple val(meta), path("*.html") , emit: report
+    path "versions.yml"           , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def fasta = genomeFasta ? "--fasta ${genomeFasta}" : ""
+    """
+    create_report $sites \
+    $args \
+    $fasta \
+    --output ${meta.id}_report.html
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        igvreports: \$(python -c "import igv_reports; print(igv_reports.__version__)")
+    END_VERSIONS
+    """
+
+    stub:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${meta.id}_report.html
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        igvreports: \$(python -c "import igv_reports; print(igv_reports.__version__)")
+    END_VERSIONS
+    """
+}

modules/nf-core/igvreports/meta.yml

@@ -0,0 +1,47 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
+name: "igvreports"
+description: A Python application to generate self-contained HTML reports for variant review and other genomic applications
+keywords:
+  - vcf
+  - variant
+  - genomics
+tools:
+  - "igvreports":
+      description: "Creates self-contained html pages for visual variant review with IGV (igv.js)."
+      homepage: "https://github.com/igvteam/igv-reports"
+      documentation: "https://github.com/igvteam/igv-reports"
+      tool_dev_url: "https://github.com/igvteam/igv-reports"
+      doi: "10.1093/bioinformatics/btac830"
+      licence: ["MIT"]
+
+input:
+  # Only when we have meta
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+
+  - sites:
+      type: file
+      description: VCF, BED, MAF, BEDPE, or generic tab delimited file of genomic variant sites
+  - genomeFasta:
+      type: file
+      description: Reference fasta file
+      pattern: "*.{fasta,fa}"
+
+output:
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+  - report:
+      type: file
+      description: html report  with a table of genomic sites and an embedded IGV genome browser for viewing data for each site
+      pattern: "*.{html}"
+
+authors:
+  - "@souljamie"
+maintainers:
+  - "@souljamie"

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

@@ -0,0 +1,107 @@
+nextflow_process {
+
+    name "Test Process IGVREPORTS"
+    script "../main.nf"
+    process "IGVREPORTS"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "igvreports"
+
+    test("testvariantsWithFasta - vcf") {
+
+        when {
+            process {
+                """
+                input[0] = [ [ id:'test'], // meta map
+                             file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true)
+                           ]
+                input[1] = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out.versions).match()},
+                {
+                    with(process.out.report) {
+                        with(get(0)) {
+                            assert get(1).endsWith("_report.html")
+                        }
+                    }
+                }
+            )
+        }
+
+    }
+
+
+
+    test("testvariantsWithGenome - vcf") {
+    config "./nextflow_genome.config"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test'], // meta map
+                     file("https://raw.githubusercontent.com/igvteam/igv-reports/master/test/data/variants/variants.vcf")
+                    ]
+                // Need to specify the empty optional fasta input
+                input[1] = []
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out.versions).match()},
+                {
+                    with(process.out.report) {
+                        with(get(0)) {
+                            assert get(1).endsWith("_report.html")
+                        }
+                    }
+                }
+            )
+        }
+
+    }
+
+    test("testvariantWithGenome - vcf - stub") {
+    config "./nextflow_genome.config"
+
+        options "-stub"
+
+        when {
+            process {
+         """
+                input[0] = [
+                    [ id:'test'], // meta map
+                     file("https://raw.githubusercontent.com/igvteam/igv-reports/master/test/data/variants/variants.vcf")
+                    ]
+                input[1] = []
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out.versions).match()},
+                {
+                    with(process.out.report) {
+                        with(get(0)) {
+                            assert get(1).endsWith("_report.html")
+                        }
+                    }
+                }
+            )
+        }
+
+    }
+
+}

modules/nf-core/igvreports/tests/nextflow_genome.config

@@ -0,0 +1,7 @@
+process {
+
+    withName: IGVREPORTS {
+        ext.args = '--genome hg38'
+    }
+
+}

modules/nf-core/igvreports/tests/tags.yml

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