gatk4_asereadcounter add updated meta and nf-tests (#5164)

* feat updated meta * feat add nf-tests * Update modules/nf-core/gatk4/asereadcounter/meta.yml Co-authored-by: Matthias Hörtenhuber <[email protected]> * Update modules/nf-core/gatk4/asereadcounter/meta.yml Co-authored-by: Matthias Hörtenhuber <[email protected]> * applyed reviewers suggestions * modified pytest_modules.yml --------- Co-authored-by: [email protected] <[email protected]> Co-authored-by: Matthias Hörtenhuber <[email protected]>
nf-core · Mar 20, 2024 · 89cf292 · 89cf292
1 parent 653218e
commit 89cf292
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diff --git a/modules/nf-core/gatk4/asereadcounter/main.nf b/modules/nf-core/gatk4/asereadcounter/main.nf
@@ -9,10 +9,10 @@ process GATK4_ASEREADCOUNTER {
 
     input:
     tuple val(meta), path(input), path(input_index)
-    tuple val(meta), path(vcf), path(tbi)
-    path fasta
-    path fai
-    path dict
+    tuple val(meta2), path(vcf), path(tbi)
+    tuple val(meta3), path(fasta)
+    tuple val(meta4), path(fai)
+    tuple val(meta5), path(dict)
     path intervals
 
     output:

diff --git a/modules/nf-core/gatk4/asereadcounter/main.nf.test b/modules/nf-core/gatk4/asereadcounter/main.nf.test
@@ -0,0 +1,54 @@
+nextflow_process {
+
+    name "Test Process GATK4_ASEREADCOUNTER"
+    tag "modules_nfcore"
+    tag "modules"
+    tag "gatk4"
+    tag "gatk4/asereadcounter"
+    script "modules/nf-core/gatk4/asereadcounter/main.nf"
+    process "GATK4_ASEREADCOUNTER"
+
+    test("Should run without failures") {
+
+        when {
+            process {
+                """
+                input[0] = [ 
+                    [ id:'test' ], // meta map
+                    file(params.modules_testdata_base_path +'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
+                    file(params.modules_testdata_base_path +'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true)
+                ]
+                input[1] = [
+                    [ id:'test' ], // meta map
+                    file(params.modules_testdata_base_path +'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path +'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true)
+                ]
+                input[2] = [
+                    [ id:'reference' ], // meta map
+                    file(params.modules_testdata_base_path +'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+                ]
+                input[3] = [
+                    [ id:'reference' ], // meta map
+                    file(params.modules_testdata_base_path +'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)
+                ]
+                input[4] = [
+                    [ id:'reference' ], // meta map
+                    file(params.modules_testdata_base_path +'genomics/sarscov2/genome/genome.dict', checkIfExists: true)
+                ]
+                input[5] = [ 
+                    file(params.modules_testdata_base_path +'genomics/sarscov2/genome/picard/targets.interval_list', checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() },
+            )
+        }
+
+    }
+
+}
diff --git a/modules/nf-core/gatk4/asereadcounter/main.nf.test.snap b/modules/nf-core/gatk4/asereadcounter/main.nf.test.snap
diff --git a/modules/nf-core/gatk4/asereadcounter/meta.yml b/modules/nf-core/gatk4/asereadcounter/meta.yml
@@ -25,18 +25,46 @@ input:
       type: file
       description: BAM/CRAM/SAM file
       pattern: "*.{bam,cram,sam}"
+  - input_index:
+      type: file
+      description: index file for input file
+      pattern: "*.{bai,crai}"
+  - meta2:
+      type: map
+      description: |
+        Groovy Map containing reference information
+        e.g. `[ id:'reference' ]`
   - vcf:
       type: file
       description: VCF file
       pattern: "*.{vcf.gz}"
+  - tbi:
+      type: file
+      description: index file for VCF file
+      pattern: "*.{vcf.gz.tbi}"
+  - meta3:
+      type: map
+      description: |
+        Groovy Map containing reference information
+        e.g. `[ id:'reference' ]`
   - fasta:
       type: file
       description: fasta file
       pattern: "*.{fasta,fa}"
+  - meta4:
+      type: map
+      description: |
+        Groovy Map containing reference information
+        e.g. `[ id:'reference' ]`
   - fai:
       type: file
       description: fasta index file
       pattern: "*.{fai}"
+  - meta5:
+      type: map
+      description: |
+        Groovy Map containing reference information
+        e.g. `[ id:'reference' ]`
   - dict:
       type: file
       description: dictionary file

diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml
@@ -697,9 +697,9 @@ gatk/unifiedgenotyper:
 gatk4/applyvqsr:
   - modules/nf-core/gatk4/applyvqsr/**
   - tests/modules/nf-core/gatk4/applyvqsr/**
-gatk4/asereadcounter:
-  - modules/nf-core/gatk4/asereadcounter/**
-  - tests/modules/nf-core/gatk4/asereadcounter/**
+gatk4/bedtointervallist:
+  - modules/nf-core/gatk4/bedtointervallist/**
+  - tests/modules/nf-core/gatk4/bedtointervallist/**
 gatk4/calculatecontamination:
   - modules/nf-core/gatk4/calculatecontamination/**
   - tests/modules/nf-core/gatk4/calculatecontamination/**

diff --git a/tests/modules/nf-core/gatk4/asereadcounter/main.nf b/tests/modules/nf-core/gatk4/asereadcounter/main.nf
diff --git a/tests/modules/nf-core/gatk4/asereadcounter/nextflow.config b/tests/modules/nf-core/gatk4/asereadcounter/nextflow.config
diff --git a/tests/modules/nf-core/gatk4/asereadcounter/test.yml b/tests/modules/nf-core/gatk4/asereadcounter/test.yml