use a check for the -fisher arg instead

nf-core · Oct 7, 2024 · f9bfe71 · f9bfe71
1 parent 398e2b1
commit f9bfe71
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Showing 5 changed files with 28 additions and 34 deletions.
diff --git a/modules/nf-core/vardictjava/main.nf b/modules/nf-core/vardictjava/main.nf
@@ -11,9 +11,6 @@ process VARDICTJAVA {
     tuple val(meta), path(bams), path(bais), path(bed)
     tuple val(meta2), path(fasta)
     tuple val(meta3), path(fasta_fai)
-    val(run_test)   // Run either teststrandbias.R or testsomatic.R. 
-                    // If this options is false the --fisher option will be added automatically
-                    // https://github.com/AstraZeneca-NGS/VarDictJava/issues/300#issuecomment-638085125
 
     output:
     tuple val(meta), path("*.vcf.gz"), emit: vcf
@@ -23,11 +20,14 @@ process VARDICTJAVA {
     task.ext.when == null || task.ext.when
 
     script:
-    def args = (task.ext.args ?: '-c 1 -S 2 -E 3') + run_test ? " --fisher" : ""
+    def args = task.ext.args ?: '-c 1 -S 2 -E 3'
     def args2 = task.ext.args2 ?: ''
     def args3 = task.ext.args3 ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
 
+    // Don't run test scripts when -fisher has been used by vardictjava
+    def run_test = !args.contains("-fisher")
+
     def somatic = bams instanceof List && bams.size() == 2 ? true : false
     def input = somatic ? "-b \"${bams[0]}|${bams[1]}\"" : "-b ${bams}"
     def test = run_test ? somatic ? "| testsomatic.R" : "| teststrandbias.R" : ""

diff --git a/modules/nf-core/vardictjava/meta.yml b/modules/nf-core/vardictjava/meta.yml
@@ -52,12 +52,6 @@ input:
         type: file
         description: The index of the FASTA of the reference genome
         pattern: "*.fai"
-  - - run_test:
-        type: boolean
-        description: |
-          Run tests using teststrandbias.R or testsomatic.R
-          When false, the --fisher option will be automatically added to the arguments
-          https://github.com/AstraZeneca-NGS/VarDictJava/issues/300#issuecomment-638085125
 output:
   - vcf:
       - meta:

diff --git a/modules/nf-core/vardictjava/tests/main.nf.test b/modules/nf-core/vardictjava/tests/main.nf.test
@@ -7,7 +7,7 @@ nextflow_process {
     tag "modules_nfcore"
     tag "vardictjava"
 
-    test("homo_sapiens - [bam, bai, bed] - fasta - fai - true") {
+    test("homo_sapiens - [bam, bai, bed] - fasta - fai") {
 
         when {
             process {
@@ -26,7 +26,6 @@ nextflow_process {
                     [id:"ref"],
                     file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)
                 ]
-                input[3] = true
                 """
             }
         }
@@ -42,7 +41,7 @@ nextflow_process {
 
     }
 
-    test("homo_sapiens - [[bam, bam], [bai, bai], bed] - fasta - fai - true") {
+    test("homo_sapiens - [[bam, bam], [bai, bai], bed] - fasta - fai") {
 
         when {
             process {
@@ -67,7 +66,6 @@ nextflow_process {
                     [id:"ref"],
                     file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)
                 ]
-                input[3] = true
                 """
             }
         }
@@ -83,8 +81,9 @@ nextflow_process {
 
     }
 
-    test("homo_sapiens - [bam, bai, bed] - fasta - fai - false") {
+    test("homo_sapiens - [bam, bai, bed] - fasta - fai - fisher") {
 
+        config "./nextflow.config"
         when {
             process {
                 """
@@ -102,7 +101,6 @@ nextflow_process {
                     [id:"ref"],
                     file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)
                 ]
-                input[3] = false
                 """
             }
         }
@@ -118,7 +116,7 @@ nextflow_process {
 
     }
 
-    test("homo_sapiens - [bam, bai, bed] - fasta - fai - true - stub") {
+    test("homo_sapiens - [bam, bai, bed] - fasta - fai - stub") {
 
         options "-stub"
 
@@ -139,7 +137,6 @@ nextflow_process {
                     [id:"ref"],
                     file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)
                 ]
-                input[3] = true
                 """
             }
         }

diff --git a/modules/nf-core/vardictjava/tests/main.nf.test.snap b/modules/nf-core/vardictjava/tests/main.nf.test.snap
@@ -1,13 +1,13 @@
 {
-    "homo_sapiens - [[bam, bam], [bai, bai], bed] - fasta - fai - true": {
+    "homo_sapiens - [bam, bai, bed] - fasta - fai": {
         "content": [
             {
                 "0": [
                     [
                         {
                             "id": "test"
                         },
-                        "test.vcf.gz:md5,7e4ab2c6d49b61c53b04e6c65c8f84ab"
+                        "test.vcf.gz:md5,e8411ecae49b4f6afa6ea0b681ea506e"
                     ]
                 ],
                 "1": [
@@ -18,7 +18,7 @@
                         {
                             "id": "test"
                         },
-                        "test.vcf.gz:md5,7e4ab2c6d49b61c53b04e6c65c8f84ab"
+                        "test.vcf.gz:md5,e8411ecae49b4f6afa6ea0b681ea506e"
                     ]
                 ],
                 "versions": [
@@ -30,17 +30,17 @@
             "nf-test": "0.9.0",
             "nextflow": "24.04.4"
         },
-        "timestamp": "2024-10-07T15:43:10.951200568"
+        "timestamp": "2024-10-07T16:05:15.117453312"
     },
-    "homo_sapiens - [bam, bai, bed] - fasta - fai - true - stub": {
+    "homo_sapiens - [[bam, bam], [bai, bai], bed] - fasta - fai": {
         "content": [
             {
                 "0": [
                     [
                         {
                             "id": "test"
                         },
-                        "test.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                        "test.vcf.gz:md5,b52c874c18be636d876d1e0df4a449c3"
                     ]
                 ],
                 "1": [
@@ -51,7 +51,7 @@
                         {
                             "id": "test"
                         },
-                        "test.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                        "test.vcf.gz:md5,b52c874c18be636d876d1e0df4a449c3"
                     ]
                 ],
                 "versions": [
@@ -63,17 +63,17 @@
             "nf-test": "0.9.0",
             "nextflow": "24.04.4"
         },
-        "timestamp": "2024-10-07T15:43:26.712061015"
+        "timestamp": "2024-10-07T16:05:26.932438089"
     },
-    "homo_sapiens - [bam, bai, bed] - fasta - fai - true": {
+    "homo_sapiens - [bam, bai, bed] - fasta - fai - fisher": {
         "content": [
             {
                 "0": [
                     [
                         {
                             "id": "test"
                         },
-                        "test.vcf.gz:md5,8acdd8ca041f024aab55d102fb6b0c38"
+                        "test.vcf.gz:md5,e8411ecae49b4f6afa6ea0b681ea506e"
                     ]
                 ],
                 "1": [
@@ -84,7 +84,7 @@
                         {
                             "id": "test"
                         },
-                        "test.vcf.gz:md5,8acdd8ca041f024aab55d102fb6b0c38"
+                        "test.vcf.gz:md5,e8411ecae49b4f6afa6ea0b681ea506e"
                     ]
                 ],
                 "versions": [
@@ -96,17 +96,17 @@
             "nf-test": "0.9.0",
             "nextflow": "24.04.4"
         },
-        "timestamp": "2024-10-07T15:43:02.162517044"
+        "timestamp": "2024-10-07T16:05:38.456816851"
     },
-    "homo_sapiens - [bam, bai, bed] - fasta - fai - false": {
+    "homo_sapiens - [bam, bai, bed] - fasta - fai - stub": {
         "content": [
             {
                 "0": [
                     [
                         {
                             "id": "test"
                         },
-                        "test.vcf.gz:md5,8acdd8ca041f024aab55d102fb6b0c38"
+                        "test.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
                     ]
                 ],
                 "1": [
@@ -117,7 +117,7 @@
                         {
                             "id": "test"
                         },
-                        "test.vcf.gz:md5,8acdd8ca041f024aab55d102fb6b0c38"
+                        "test.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
                     ]
                 ],
                 "versions": [
@@ -129,6 +129,6 @@
             "nf-test": "0.9.0",
             "nextflow": "24.04.4"
         },
-        "timestamp": "2024-10-07T15:43:19.212653351"
+        "timestamp": "2024-10-07T16:05:48.440804849"
     }
 }
diff --git a/modules/nf-core/vardictjava/tests/nextflow.config b/modules/nf-core/vardictjava/tests/nextflow.config
@@ -0,0 +1,3 @@
+process {
+    ext.args = "-c 1 -S 2 -E 3 -fisher"
+}