Fix issue with STAR signal module

guigolab · Apr 30, 2024 · acb6b52 · acb6b52
1 parent 1d11dc8
commit acb6b52
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Showing 5 changed files with 104 additions and 9 deletions.
diff --git a/modules/bigwig/star/main.nf b/modules/bigwig/star/main.nf
@@ -31,7 +31,7 @@ process signal {
     """
 }
 
-process bigwig {
+process bw {
 
     tag "${sample}"
     container params.bgtobwContainer
@@ -89,3 +89,16 @@ process bigwig {
     }
     cmd.join('\n')
 }
+
+workflow bigwig {
+    take:
+      fastaIndex
+      genomeAlignments
+
+    main:
+      signal( fastaIndex, genomeAlignments )
+      bw( fastaIndex, signal.out )
+
+    emit:
+      bw.out
+}
diff --git a/tests/modules/bigwig/star/main.bigwig.nf.test b/tests/modules/bigwig/star/main.bigwig.nf.test
@@ -2,7 +2,7 @@ nextflow_process {
 
     name "Test Process bigwig"
     script "modules/bigwig/star/main.nf"
-    process "bigwig"
+    process "bw"
 
     tag "module"
 

diff --git a/tests/workflows/signal.nf.test b/tests/workflows/signal.nf.test
@@ -6,7 +6,7 @@ nextflow_workflow {
 
     tag "workflow"
 
-    test("Should produce bigwig files") {
+    test("Should produce bigwig files with STAR") {
 
         when {
             params {
@@ -32,6 +32,32 @@ nextflow_workflow {
 
     }
 
+    test("Should produce bigwig files with RGCRG") {
+
+        when {
+            params {
+                fastaIndexTool = "samtools"
+                contigTool = "rgcrg"
+                bigwigTool = "rgcrg"
+                stepList = ['bigwig']
+            }
+            workflow {
+                """
+                input[0] = file("${baseDir}/data/genome.fa.gz")
+                input[1] = Channel.from([
+                    [ "sample3", "test3", file("${baseDir}/data/sample3_m4_n10_toGenome.bam"), "bam", "GenomeAlignments", true, "MATE2_SENSE"]
+                ])
+                """
+            }
+        }
+
+        then {
+            assert workflow.success
+            assert snapshot(workflow.out).match()
+        }
+
+    }
+
     test("Should produce contig files") {
 
         when {

diff --git a/tests/workflows/signal.nf.test.snap b/tests/workflows/signal.nf.test.snap
@@ -36,9 +36,66 @@
             "nf-test": "0.8.4",
             "nextflow": "23.10.1"
         },
-        "timestamp": "2024-04-25T14:05:02.995265"
+        "timestamp": "2024-04-30T18:20:00.779747"
     },
-    "Should produce bigwig files": {
+    "Should produce bigwig files with RGCRG": {
+        "content": [
+            {
+                "0": [
+
+                ],
+                "1": [
+                    [
+                        "sample3",
+                        "test3",
+                        "sample3.minusRaw.bw:md5,db10a50bb7eebec0f3421f4460d4cae8",
+                        "bigWig",
+                        "MinusRawSignal",
+                        true,
+                        "MATE2_SENSE"
+                    ],
+                    [
+                        "sample3",
+                        "test3",
+                        "sample3.plusRaw.bw:md5,235e2d65c856c969048e432234c04ff4",
+                        "bigWig",
+                        "PlusRawSignal",
+                        true,
+                        "MATE2_SENSE"
+                    ]
+                ],
+                "bigwigs": [
+                    [
+                        "sample3",
+                        "test3",
+                        "sample3.minusRaw.bw:md5,db10a50bb7eebec0f3421f4460d4cae8",
+                        "bigWig",
+                        "MinusRawSignal",
+                        true,
+                        "MATE2_SENSE"
+                    ],
+                    [
+                        "sample3",
+                        "test3",
+                        "sample3.plusRaw.bw:md5,235e2d65c856c969048e432234c04ff4",
+                        "bigWig",
+                        "PlusRawSignal",
+                        true,
+                        "MATE2_SENSE"
+                    ]
+                ],
+                "contigs": [
+
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-04-30T18:14:51.685863"
+    },
+    "Should produce bigwig files with STAR": {
         "content": [
             {
                 "0": [
@@ -129,6 +186,6 @@
             "nf-test": "0.8.4",
             "nextflow": "23.10.1"
         },
-        "timestamp": "2024-04-25T14:04:52.79812"
+        "timestamp": "2024-04-30T18:20:54.929343"
     }
 }
diff --git a/workflows/signal.nf b/workflows/signal.nf
@@ -1,6 +1,6 @@
 include { fastaIndex } from "../modules/fastaIndex/${params.fastaIndexTool}"
 include { contig } from "../modules/contig/${params.contigTool.toLowerCase()}"
-include { signal as bedgraph; bigwig } from "../modules/bigwig/${params.bigwigTool.toLowerCase()}"
+include { bigwig } from "../modules/bigwig/${params.bigwigTool.toLowerCase()}"
 
 doBigwig = ( 'bigwig' in params.stepList )
 doContig = ( 'contig' in params.stepList )
@@ -15,8 +15,7 @@ workflow signal {
         fastaIndex( genome )
       }
       if ( doBigwig ) {
-        bedgraph( fastaIndex.out, genomeAlignments )
-        bigwig( fastaIndex.out, bedgraph.out )
+        bigwig( fastaIndex.out, genomeAlignments )
       }
       if ( doContig ) {
         contig( fastaIndex.out, genomeAlignments )