change name to star/indexversion

nf-core · Feb 25, 2025 · cfcc9c4 · cfcc9c4
1 parent 3d241a1
commit cfcc9c4
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Showing 6 changed files with 63 additions and 63 deletions.
diff --git a/modules/nf-core/star/help/tests/main.nf.test.snap b/modules/nf-core/star/help/tests/main.nf.test.snap
diff --git a/modules/nf-core/star/help/environment.yml → ...nf-core/star/indexversion/environment.yml b/modules/nf-core/star/help/environment.yml → ...nf-core/star/indexversion/environment.yml
diff --git a/modules/nf-core/star/help/main.nf → modules/nf-core/star/indexversion/main.nf b/modules/nf-core/star/help/main.nf → modules/nf-core/star/indexversion/main.nf
@@ -1,4 +1,4 @@
-process STAR_HELP {
+process STAR_INDEXVERSION {
     label 'process_single'
 
     conda "${moduleDir}/environment.yml"
@@ -7,16 +7,16 @@ process STAR_HELP {
         'community.wave.seqera.io/library/htslib_samtools_star_gawk:ae438e9a604351a4' }"
 
     output:
-    path("*.txt")       , emit: help
+    path("*.txt")       , emit: index_version
     path "versions.yml" , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
 
     script:
-    def prefix = task.ext.prefix ?: "help"
+    def prefix = task.ext.prefix ?: "index_version"
     """
-    STAR --help > ${prefix}.txt
+    STAR --help | grep 'versionGenome' | sed -e 's/versionGenome[ \t]*//' | sed -e 's/ .*//'  > ${prefix}.txt
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
@@ -27,9 +27,9 @@ process STAR_HELP {
     """
 
     stub:
-    def prefix = task.ext.prefix ?: "help"
+    def prefix = task.ext.prefix ?: "index_version"
     """
-    STAR --help > ${prefix}.txt
+    STAR --help | grep 'versionGenome' | sed -e 's/versionGenome[ \t]*//' | sed -e 's/ .*//'  > ${prefix}.txt
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

diff --git a/modules/nf-core/star/help/meta.yml → modules/nf-core/star/indexversion/meta.yml b/modules/nf-core/star/help/meta.yml → modules/nf-core/star/indexversion/meta.yml
@@ -1,10 +1,10 @@
 ---
 # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
-name: "star_help"
-description: Get the help message from STAR
+name: "star_indexversion"
+description: Get the minimal allowed index version from STAR
 keywords:
-  - help
-  - message
+  - index
+  - version
   - rna
 tools:
   - star:
@@ -18,10 +18,10 @@ tools:
       identifier: biotools:star
 
 output:
-  - help:
+  - index_version:
     - "*.txt":
         type: file
-        description: File with the help message
+        description: File with the minimal index version
         pattern: "*.txt"
 
   - versions:

diff --git a/modules/nf-core/star/help/tests/main.nf.test → ...core/star/indexversion/tests/main.nf.test b/modules/nf-core/star/help/tests/main.nf.test → ...core/star/indexversion/tests/main.nf.test
@@ -1,13 +1,13 @@
 nextflow_process {
 
-    name "Test Process STAR_HELP"
+    name "Test Process STAR_INDEXVERSION"
     script "../main.nf"
-    process "STAR_HELP"
+    process "STAR_INDEXVERSION"
 
     tag "modules"
     tag "modules_nfcore"
     tag "star"
-    tag "star/help"
+    tag "star/indexversion"
 
     test("normal run") {
 

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"
+    }
+}