fix: Make sure the gtf is unzipped

nf-core · Apr 27, 2024 · 9940414 · 9940414
1 parent ca68e9b
commit 9940414
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Showing 3 changed files with 32 additions and 1 deletion.
diff --git a/workflows/nascent.nf b/workflows/nascent.nf
@@ -200,7 +200,10 @@ workflow NASCENT {
         ch_versions = ch_versions.mix(FASTQ_ALIGN_HISAT2.out.versions)
     } else if (!params.skip_alignment && params.aligner == 'star') {
         if(!ch_star_index) {
-            ch_star_index = STAR_GENOMEGENERATE ( ch_fasta, [ [:], ch_gtf ] ).index
+            ch_star_index = STAR_GENOMEGENERATE (
+                ch_fasta,
+                PREPARE_GENOME.out.gtf.map { [[:], it] }
+            ).index
         } else if (ch_star_index.endsWith('.tar.gz')) {
             ch_star_index = UNTAR_STAR_INDEX ( [ [:], ch_star_index ] ).untar
             ch_versions = ch_versions.mix(UNTAR_STAR_INDEX.out.versions)

diff --git a/workflows/tests/star.nf.test b/workflows/tests/star.nf.test
@@ -21,4 +21,22 @@ nextflow_pipeline {
             ).match()
         }
     }
+
+    test("Should run with gzipped gtf") {
+
+        when {
+            params {
+                outdir = "$outputDir"
+                aligner = "star"
+                gtf = "https://raw.githubusercontent.com/nf-core/test-datasets/nascent/reference/genes_chr21.gtf.gz"
+            }
+        }
+
+        then {
+            assert workflow.success
+            assert snapshot(
+                workflow.trace.tasks().size(),
+            ).match()
+        }
+    }
 }
diff --git a/workflows/tests/star.nf.test.snap b/workflows/tests/star.nf.test.snap
@@ -1,4 +1,14 @@
 {
+    "Should run with gzipped gtf": {
+        "content": [
+            140
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.03.0"
+        },
+        "timestamp": "2024-04-27T12:40:13.788464472"
+    },
     "Should run with STAR (default)": {
         "content": [
             139