IGV Snapshot module

.github/workflows/test.yml

@@ -416,6 +416,8 @@ jobs:
             tags: salmon/quant
           - profile: "conda"
             tags: rediscoverte
+          - profile: "conda"
+            tags: igv/snapshot
 
     env:
       NXF_ANSI_LOG: false

modules/msk/igv/snapshot/environment.yml

@@ -0,0 +1,9 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+name: "igv_snapshot"
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - "bioconda::igv=2.17.4"

modules/msk/igv/snapshot/main.nf

@@ -0,0 +1,57 @@
+process IGV_SNAPSHOT {
+    tag "$meta.id"
+    label 'process_single'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'ghcr.io/msk-access/igv_snapshot:0.0.1':
+        'ghcr.io/msk-access/igv_snapshot:0.0.1' }"
+
+    input:
+    tuple val(meta), path(bam), path(bai), path(variant_file)
+
+    output:
+
+    tuple val(meta), path("**igv_output/*"), emit: igv_screenshots
+    path "versions.yml"           , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ""
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def bed_name = prefix ? "${prefix}.bed": "variant.bed"
+    def out = prefix ? "${prefix}_igv_output": "igv_output"
+    def genome = task.ext.genome ? "-g ${task.ext.genome}" : ""
+    """
+    igv run_screenshot \\
+    --input-files $bam \\
+    --annotated-variant-file $variant_file \\
+    -t $prefix \\
+    -o $out \\
+    -r $bed_name \\
+    $genome
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        igv: \$(igv --version)
+    END_VERSIONS
+    """
+
+    stub:
+    def args = task.ext.args ?: ""
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def bed_name = prefix ? "${prefix}.bed": "variant.bed"
+    def out = prefix ? "${prefix}_igv_output": "igv_output"
+    """
+    mkdir $out
+    touch $out/test.png
+    touch $out/test.bat
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        igv: \$(igv --version)
+    END_VERSIONS
+    """
+}

modules/msk/igv/snapshot/meta.yml

@@ -0,0 +1,62 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
+name: "igv_snapshot"
+description: a module to run IGV screenshot
+keywords:
+  - sort
+  - example
+  - genomics
+tools:
+  - "igv":
+      description: "Integrative Genomics Viewer. Fast, efficient, scalable visualization tool for genomics data and annotations."
+      homepage: "https://igv.org/"
+      documentation: "https://igv.org/doc/desktop/#QuickStart/"
+      tool_dev_url: "https://github.com/igvteam/igv"
+      licence: ["MIT"]
+  - "igv snapshot":
+      description: "A python package to generate and execute IGV screenshot script."
+      documentation: "https://github.com/msk-access/igv_snapshot/blob/main/README.md"
+      tool_dev_url: "https://github.com/msk-access/igv_snapshot"
+      licence: ["MIT"]
+
+input:
+  # Only when we have meta
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. `[ id:'sample1', single_end:false ]`
+  - bam:
+      type: file
+      description: BAM file with index.
+      pattern: "*.{bam,cram,sam}"
+  - bai:
+      type: file
+      description: BAM file index
+      pattern: "*.{bai}"
+  - variant_file:
+      type: file
+      description: Variant file of input BAM.
+      pattern: "*.{maf,vcf}"
+
+output:
+  #Only when we have meta
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. `[ id:'sample1', single_end:false ]`
+
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+  - igv_screenshots:
+      type: directory
+      description: directory containing IGV screenshot for provided sample, and the bat script used to generate the screenshots.
+      pattern: "**igv_output/*"
+
+authors:
+  - "@buehlere"
+maintainers:
+  - "@buehlere"

modules/msk/igv/snapshot/tests/main.nf.test

@@ -0,0 +1,64 @@
+nextflow_process {
+
+    name "Test Process IGV_SNAPSHOT"
+    script "../main.nf"
+    process "IGV_SNAPSHOT"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "modules_msk"
+    tag "igv"
+    tag "igv/snapshot"
+
+    test("chr22 - bam, vcf") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'C-9M47TU-L001-d'], // meta map
+                    file(params.test_data_mskcc['chr22']['chr22bam'], checkIfExists: true),
+                    file(params.test_data_mskcc['chr22']['chr22bam_bai'], checkIfExists: true),
+                    file(params.test_data_mskcc['chr22']['chr22vcf'], checkIfExists: true)
+
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+    test("chr22 - bam, vcf - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'C-9M47TU-L001-d'], // meta map
+                    file(params.test_data_mskcc['chr22']['chr22bam'], checkIfExists: true),
+                    file(params.test_data_mskcc['chr22']['chr22bam_bai'], checkIfExists: true),
+                    file(params.test_data_mskcc['chr22']['chr22vcf'], checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+}

modules/msk/igv/snapshot/tests/main.nf.test.snap

@@ -0,0 +1,82 @@
+{
+    "chr22 - bam, vcf - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "C-9M47TU-L001-d"
+                        },
+                        [
+                            "test.bat:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test.png:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        ]
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,870a90d9f64f5a5f5ec4cd474d69027c"
+                ],
+                "igv_screenshots": [
+                    [
+                        {
+                            "id": "C-9M47TU-L001-d"
+                        },
+                        [
+                            "test.bat:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test.png:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        ]
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,870a90d9f64f5a5f5ec4cd474d69027c"
+                ]
+            }
+        ],
+        "timestamp": "2024-08-06T17:08:44.477177"
+    },
+    "chr22 - bam, vcf": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "C-9M47TU-L001-d"
+                        },
+                        [
+                            "22_22127176_22127176.png:md5,fd9de31a371db4523f8a0982df749a09",
+                            "22_41565827_41565827.png:md5,1904ecf0b28baeee6e14e78543052a17",
+                            "22_41566406_41566406.png:md5,c77c48716ed2272f45b49c7852a74705",
+                            "22_41566413_41566413.png:md5,bfaf4189292aa0495e51c26ea33f64f7",
+                            "22_41566595_41566595.png:md5,2fca6b6e75fd4c533fb512d0cd11941b",
+                            "22_41566657_41566657.png:md5,fd49c1c6439206da9c15595921392d29",
+                            "IGV_snapshots.bat:md5,d2eaf7a013f62e5fe07f8a0ddf459ace"
+                        ]
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,870a90d9f64f5a5f5ec4cd474d69027c"
+                ],
+                "igv_screenshots": [
+                    [
+                        {
+                            "id": "C-9M47TU-L001-d"
+                        },
+                        [
+                            "22_22127176_22127176.png:md5,fd9de31a371db4523f8a0982df749a09",
+                            "22_41565827_41565827.png:md5,1904ecf0b28baeee6e14e78543052a17",
+                            "22_41566406_41566406.png:md5,c77c48716ed2272f45b49c7852a74705",
+                            "22_41566413_41566413.png:md5,bfaf4189292aa0495e51c26ea33f64f7",
+                            "22_41566595_41566595.png:md5,2fca6b6e75fd4c533fb512d0cd11941b",
+                            "22_41566657_41566657.png:md5,fd49c1c6439206da9c15595921392d29",
+                            "IGV_snapshots.bat:md5,d2eaf7a013f62e5fe07f8a0ddf459ace"
+                        ]
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,870a90d9f64f5a5f5ec4cd474d69027c"
+                ]
+            }
+        ],
+        "timestamp": "2024-08-06T17:08:31.32318"
+    }
+}

modules/msk/igv/snapshot/tests/tags.yml

@@ -0,0 +1,2 @@
+igv/snapshot:
+  - "modules/msk/igv/snapshot/**"

tests/config/test_data.config

@@ -725,6 +725,9 @@ params {
                 dbsnp_138_b37_chr17_vcf_gz_tbi                 = "${params.test_data_base_msk}/hg37/genomic_reference/GRCH37/vcf/dbsnp_138.b37.chr17.vcf.gz.tbi"
             }
             'chr22' {
+                chr22bam                                       = "${params.test_data_base_msk}/chr22/chr22/chr22.bam"
+                chr22bam_bai                                   = "${params.test_data_base_msk}/chr22/chr22/chr22.bam.bai"
+                chr22vcf                                       = "${params.test_data_base_msk}/chr22/chr22/chr22.vcf"
                 chr22maf                                       = "${params.test_data_base_msk}/chr22/chr22/chr22.maf"
                 chr22mafstandard                               = "${params.test_data_base_msk}/chr22/chr22/chr22_standard.maf"
                 }