new module: star/indexversion (#7512)

* new module: star/help * update env.yml * change name to star/indexversion
nf-core · Feb 25, 2025 · 752700e · 752700e
1 parent c6169fa
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diff --git a/modules/nf-core/star/indexversion/environment.yml b/modules/nf-core/star/indexversion/environment.yml
@@ -0,0 +1,10 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - bioconda::htslib=1.21
+  - bioconda::samtools=1.21
+  - bioconda::star=2.7.11b
+  - conda-forge::gawk=5.1.0
diff --git a/modules/nf-core/star/indexversion/main.nf b/modules/nf-core/star/indexversion/main.nf
@@ -0,0 +1,41 @@
+process STAR_INDEXVERSION {
+    label 'process_single'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/26/268b4c9c6cbf8fa6606c9b7fd4fafce18bf2c931d1a809a0ce51b105ec06c89d/data' :
+        'community.wave.seqera.io/library/htslib_samtools_star_gawk:ae438e9a604351a4' }"
+
+    output:
+    path("*.txt")       , emit: index_version
+    path "versions.yml" , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def prefix = task.ext.prefix ?: "index_version"
+    """
+    STAR --help | grep 'versionGenome' | sed -e 's/versionGenome[ \t]*//' | sed -e 's/ .*//'  > ${prefix}.txt
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        star: \$(STAR --version | sed -e "s/STAR_//g")
+        samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
+        gawk: \$(echo \$(gawk --version 2>&1) | sed 's/^.*GNU Awk //; s/, .*\$//')
+    END_VERSIONS
+    """
+
+    stub:
+    def prefix = task.ext.prefix ?: "index_version"
+    """
+    STAR --help | grep 'versionGenome' | sed -e 's/versionGenome[ \t]*//' | sed -e 's/ .*//'  > ${prefix}.txt
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        star: \$(STAR --version | sed -e "s/STAR_//g")
+        samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
+        gawk: \$(echo \$(gawk --version 2>&1) | sed 's/^.*GNU Awk //; s/, .*\$//')
+    END_VERSIONS
+    """
+}
diff --git a/modules/nf-core/star/indexversion/meta.yml b/modules/nf-core/star/indexversion/meta.yml
@@ -0,0 +1,36 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
+name: "star_indexversion"
+description: Get the minimal allowed index version from STAR
+keywords:
+  - index
+  - version
+  - rna
+tools:
+  - star:
+      description: |
+        STAR is a software package for mapping DNA sequences against
+        a large reference genome, such as the human genome.
+      homepage: https://github.com/alexdobin/STAR
+      manual: https://github.com/alexdobin/STAR/blob/master/doc/STARmanual.pdf
+      doi: 10.1093/bioinformatics/bts635
+      licence: ["MIT"]
+      identifier: biotools:star
+
+output:
+  - index_version:
+    - "*.txt":
+        type: file
+        description: File with the minimal index version
+        pattern: "*.txt"
+
+  - versions:
+    - "versions.yml":
+        type: file
+        description: File containing software versions
+        pattern: "versions.yml"
+
+authors:
+  - "@nvnieuwk"
+maintainers:
+  - "@nvnieuwk"
diff --git a/modules/nf-core/star/indexversion/tests/main.nf.test b/modules/nf-core/star/indexversion/tests/main.nf.test
@@ -0,0 +1,36 @@
+nextflow_process {
+
+    name "Test Process STAR_INDEXVERSION"
+    script "../main.nf"
+    process "STAR_INDEXVERSION"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "star"
+    tag "star/indexversion"
+
+    test("normal run") {
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+    test("stub run") {
+
+        options "-stub"
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+}
diff --git a/modules/nf-core/star/indexversion/tests/main.nf.test.snap b/modules/nf-core/star/indexversion/tests/main.nf.test.snap
@@ -0,0 +1,48 @@
+{
+    "normal run": {
+        "content": [
+            {
+                "0": [
+                    "index_version.txt:md5,184a6b325b4ac98bd08ffc0bd8f046cd"
+                ],
+                "1": [
+                    "versions.yml:md5,003e8e66b98a702010f209d5049eeabc"
+                ],
+                "index_version": [
+                    "index_version.txt:md5,184a6b325b4ac98bd08ffc0bd8f046cd"
+                ],
+                "versions": [
+                    "versions.yml:md5,003e8e66b98a702010f209d5049eeabc"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.4"
+        },
+        "timestamp": "2025-02-25T13:06:11.149770431"
+    },
+    "stub run": {
+        "content": [
+            {
+                "0": [
+                    "index_version.txt:md5,184a6b325b4ac98bd08ffc0bd8f046cd"
+                ],
+                "1": [
+                    "versions.yml:md5,003e8e66b98a702010f209d5049eeabc"
+                ],
+                "index_version": [
+                    "index_version.txt:md5,184a6b325b4ac98bd08ffc0bd8f046cd"
+                ],
+                "versions": [
+                    "versions.yml:md5,003e8e66b98a702010f209d5049eeabc"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.4"
+        },
+        "timestamp": "2025-02-25T13:06:16.834272136"
+    }
+}