Add hostile/fetch (#6949)

* Add hostile/fetch * [automated] Fix linting with Prettier * Fix nf-core linting * fix stub test * Fix stub version generation and md5sum * Update modules/nf-core/hostile/fetch/meta.yml --------- Co-authored-by: nf-core-bot <[email protected]> Co-authored-by: Sateesh <[email protected]> Co-authored-by: Sateesh_Peri <[email protected]>
nf-core · Nov 7, 2024 · a2db453 · a2db453
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diff --git a/modules/nf-core/hostile/fetch/environment.yml b/modules/nf-core/hostile/fetch/environment.yml
@@ -0,0 +1,7 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - "bioconda::hostile=1.1.0"
diff --git a/modules/nf-core/hostile/fetch/main.nf b/modules/nf-core/hostile/fetch/main.nf
@@ -0,0 +1,50 @@
+process HOSTILE_FETCH {
+    label 'process_single'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/hostile:1.1.0--pyhdfd78af_0':
+        'biocontainers/hostile:1.1.0--pyhdfd78af_0' }"
+
+    output:
+    path "reference/"   , emit: reference
+    path "versions.yml" , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    """
+    mkdir reference/
+    export HOSTILE_CACHE_DIR=./reference
+
+    hostile \\
+        fetch \\
+        ${args}
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        hostile: \$(hostile --version)
+    END_VERSIONS
+    """
+
+    stub:
+    def args = task.ext.args ?: ''
+    """
+    mkdir reference/
+    export HOSTILE_CACHE_DIR=./reference
+
+    touch reference/human-t2t-hla.1.bt2
+    touch reference/human-t2t-hla.2.bt2
+    touch reference/human-t2t-hla.3.bt2
+    touch reference/human-t2t-hla.4.bt2
+    touch reference/human-t2t-hla.rev.1.bt2
+    touch reference/human-t2t-hla.rev.2.bt2
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        hostile: \$(hostile --version)
+    END_VERSIONS
+    """
+}
diff --git a/modules/nf-core/hostile/fetch/meta.yml b/modules/nf-core/hostile/fetch/meta.yml
@@ -0,0 +1,38 @@
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
+name: "hostile_fetch"
+description: Downloads required reference genomes for Hostile
+keywords:
+  - hostile
+  - decontamination
+  - human removal
+  - download
+tools:
+  - "hostile":
+      description: "Hostile: accurate host decontamination"
+      homepage: "https://github.com/bede/hostile"
+      documentation: "https://github.com/bede/hostile"
+      tool_dev_url: "https://github.com/bede/hostile"
+      doi: "10.1093/bioinformatics/btad728"
+      licence: ["MIT"]
+      identifier: biotools:hostile
+
+output:
+  - reference:
+      - "reference/":
+          type: directory
+          description: Directory containing required reference genome files
+            for hostile clean
+          pattern: "reference/"
+          ontologies:
+            - edam: "http://edamontology.org/data_1049"
+
+  - versions:
+      - "versions.yml":
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
+
+authors:
+  - "@jfy133"
+maintainers:
+  - "@jfy133"
diff --git a/modules/nf-core/hostile/fetch/tests/main.nf.test b/modules/nf-core/hostile/fetch/tests/main.nf.test
@@ -0,0 +1,50 @@
+nextflow_process {
+
+    name "Test Process HOSTILE_FETCH"
+    script "../main.nf"
+    process "HOSTILE_FETCH"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "hostile"
+    tag "hostile/fetch"
+
+    test("default") {
+
+        when {
+            process {
+                """
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+    test("default - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+}
diff --git a/modules/nf-core/hostile/fetch/tests/main.nf.test.snap b/modules/nf-core/hostile/fetch/tests/main.nf.test.snap
@@ -0,0 +1,78 @@
+{
+    "default": {
+        "content": [
+            {
+                "0": [
+                    [
+                        "human-t2t-hla.1.bt2:md5,b481b623a14908f29c5dce42077f8763",
+                        "human-t2t-hla.2.bt2:md5,8df357276c7c3a4e768ecd70ca951b53",
+                        "human-t2t-hla.3.bt2:md5,78289afb436f8d0a9526ecfa95e3fa24",
+                        "human-t2t-hla.4.bt2:md5,198badf146cd0b3886b674424250d419",
+                        "human-t2t-hla.fa.gz:md5,65dfdc3245d5a34616e71c999e0a49d7",
+                        "human-t2t-hla.rev.1.bt2:md5,34c65db94aba9cc49cb31e14d2698c1c",
+                        "human-t2t-hla.rev.2.bt2:md5,53c9901609915475a2e1b009046d8371"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,946753059fc7eb42e87c6e22a8bbfd7b"
+                ],
+                "reference": [
+                    [
+                        "human-t2t-hla.1.bt2:md5,b481b623a14908f29c5dce42077f8763",
+                        "human-t2t-hla.2.bt2:md5,8df357276c7c3a4e768ecd70ca951b53",
+                        "human-t2t-hla.3.bt2:md5,78289afb436f8d0a9526ecfa95e3fa24",
+                        "human-t2t-hla.4.bt2:md5,198badf146cd0b3886b674424250d419",
+                        "human-t2t-hla.fa.gz:md5,65dfdc3245d5a34616e71c999e0a49d7",
+                        "human-t2t-hla.rev.1.bt2:md5,34c65db94aba9cc49cb31e14d2698c1c",
+                        "human-t2t-hla.rev.2.bt2:md5,53c9901609915475a2e1b009046d8371"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,946753059fc7eb42e87c6e22a8bbfd7b"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.1",
+            "nextflow": "24.10.0"
+        },
+        "timestamp": "2024-11-07T12:49:16.503252839"
+    },
+    "default - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        "human-t2t-hla.1.bt2:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "human-t2t-hla.2.bt2:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "human-t2t-hla.3.bt2:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "human-t2t-hla.4.bt2:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "human-t2t-hla.rev.1.bt2:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "human-t2t-hla.rev.2.bt2:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,946753059fc7eb42e87c6e22a8bbfd7b"
+                ],
+                "reference": [
+                    [
+                        "human-t2t-hla.1.bt2:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "human-t2t-hla.2.bt2:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "human-t2t-hla.3.bt2:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "human-t2t-hla.4.bt2:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "human-t2t-hla.rev.1.bt2:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "human-t2t-hla.rev.2.bt2:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,946753059fc7eb42e87c6e22a8bbfd7b"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.10.0"
+        },
+        "timestamp": "2024-11-07T14:53:24.640950662"
+    }
+}