nf-test + update to genotypegvcfs (#6553)

* nf-test + update to genotypegvcfs * fix linting * review comments * fix old typo * Update modules/nf-core/gatk4/genotypegvcfs/meta.yml Co-authored-by: Felix Lenner <[email protected]> * Update modules/nf-core/gatk4/genotypegvcfs/meta.yml Co-authored-by: Felix Lenner <[email protected]> * Update modules/nf-core/gatk4/genotypegvcfs/meta.yml Co-authored-by: Felix Lenner <[email protected]> * Update modules/nf-core/gatk4/genotypegvcfs/meta.yml Co-authored-by: Felix Lenner <[email protected]> * Update modules/nf-core/gatk4/genotypegvcfs/meta.yml Co-authored-by: Felix Lenner <[email protected]> --------- Co-authored-by: Felix Lenner <[email protected]>
nf-core · Sep 5, 2024 · 8b74c80 · 8b74c80
1 parent 51d4916
commit 8b74c80
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Showing 8 changed files with 512 additions and 324 deletions.
diff --git a/modules/nf-core/gatk4/genotypegvcfs/main.nf b/modules/nf-core/gatk4/genotypegvcfs/main.nf
@@ -8,12 +8,12 @@ process GATK4_GENOTYPEGVCFS {
         'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }"
 
     input:
-    tuple val(meta), path(gvcf), path(gvcf_index), path(intervals), path(intervals_index)
-    path  fasta
-    path  fai
-    path  dict
-    path  dbsnp
-    path  dbsnp_tbi
+    tuple val(meta), path(input), path(gvcf_index), path(intervals), path(intervals_index)
+    tuple val(meta2), path(fasta)
+    tuple val(meta3), path(fai)
+    tuple val(meta4), path(dict)
+    tuple val(meta5), path(dbsnp)
+    tuple val(meta6), path(dbsnp_tbi)
 
     output:
     tuple val(meta), path("*.vcf.gz"), emit: vcf
@@ -26,7 +26,7 @@ process GATK4_GENOTYPEGVCFS {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def gvcf_command = gvcf.name.endsWith(".vcf") || gvcf.name.endsWith(".vcf.gz") ? "$gvcf" : "gendb://$gvcf"
+    def input_command = input.name.endsWith(".vcf") || input.name.endsWith(".vcf.gz") ? "$input" : "gendb://$input"
     def dbsnp_command = dbsnp ? "--dbsnp $dbsnp" : ""
     def interval_command = intervals ? "--intervals $intervals" : ""
 
@@ -39,7 +39,7 @@ process GATK4_GENOTYPEGVCFS {
     """
     gatk --java-options "-Xmx${avail_mem}M -XX:-UsePerfData" \\
         GenotypeGVCFs \\
-        --variant $gvcf_command \\
+        --variant $input_command \\
         --output ${prefix}.vcf.gz \\
         --reference $fasta \\
         $interval_command \\
@@ -57,7 +57,7 @@ process GATK4_GENOTYPEGVCFS {
     def prefix = task.ext.prefix ?: "${meta.id}"
 
     """
-    touch ${prefix}.vcf.gz
+    echo | gzip > ${prefix}.vcf.gz
     touch ${prefix}.vcf.gz.tbi
 
     cat <<-END_VERSIONS > versions.yml

diff --git a/modules/nf-core/gatk4/genotypegvcfs/meta.yml b/modules/nf-core/gatk4/genotypegvcfs/meta.yml
@@ -20,10 +20,10 @@ input:
       description: |
         Groovy Map containing sample information
         e.g. [ id:'test', single_end:false ]
-  - gvcf:
+  - input:
       type: file
       description: |
-        gVCF(.gz) file or to a GenomicsDB
+        gVCF(.gz) file or a GenomicsDB
       pattern: "*.{vcf,vcf.gz}"
   - gvcf_index:
       type: file
@@ -36,22 +36,47 @@ input:
   - intervals_index:
       type: file
       description: Interval index file (optional)
+  - meta2:
+      type: map
+      description: |
+        Groovy Map containing fasta information
+        e.g. [ id:'test' ]
   - fasta:
       type: file
       description: Reference fasta file
       pattern: "*.fasta"
+  - meta3:
+      type: map
+      description: |
+        Groovy Map containing fai information
+        e.g. [ id:'test' ]
   - fai:
       type: file
       description: Reference fasta index file
       pattern: "*.fai"
+  - meta4:
+      type: map
+      description: |
+        Groovy Map containing dict information
+        e.g. [ id:'test' ]
   - dict:
       type: file
       description: Reference fasta sequence dict file
       pattern: "*.dict"
+  - meta5:
+      type: map
+      description: |
+        Groovy Map containing dbsnp information
+        e.g. [ id:'test' ]
   - dbsnp:
       type: file
       description: dbSNP VCF file
       pattern: "*.vcf.gz"
+  - meta6:
+      type: map
+      description: |
+        Groovy Map containing dbsnp tbi information
+        e.g. [ id:'test' ]
   - dbsnp_tbi:
       type: file
       description: dbSNP VCF index file

diff --git a/modules/nf-core/gatk4/genotypegvcfs/tests/main.nf.test b/modules/nf-core/gatk4/genotypegvcfs/tests/main.nf.test
@@ -0,0 +1,285 @@
+nextflow_process {
+
+    name "Test Process GATK4_GENOTYPEGVCFS"
+    script "../main.nf"
+    process "GATK4_GENOTYPEGVCFS"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "gatk4"
+    tag "gatk4/genotypegvcfs"
+    tag "untar"
+
+    setup {
+        run("UNTAR") {
+            script "../../../untar/main.nf"
+            process {
+                """
+                input[0] = [
+                    [id:"test"],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/test_genomicsdb.tar.gz', checkIfExists: true)
+                ]
+                """
+            }
+        }
+    }
+
+    test("homo_sapiens - [gvcf, idx, [], []], fasta, fai, dict, [], []") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [id:"test"],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.idx', checkIfExists: true),
+                    [],
+                    []
+                ]
+                input[1] = [
+                    [id:"fasta"],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists:true)
+                ]
+                input[2] = [
+                    [id:"fai"],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists:true)
+                ]
+                input[3] = [
+                    [id:"dict"],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.dict', checkIfExists:true)
+                ]
+                input[4] = [[],[]]
+                input[5] = [[],[]]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    process.out.vcf.collect { [it[0], path(it[1]).vcf.variantsMD5] },
+                    process.out.tbi.collect { [it[0], file(it[1]).name] },
+                    process.out.versions
+                ).match() }
+            )
+        }
+
+    }
+
+    test("homo_sapiens - [gvcf_gz, tbi, [], []], fasta, fai, dict, dbsnp, dbsnp_tbi") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [id:"test"],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz.tbi', checkIfExists: true),
+                    [],
+                    []
+                ]
+                input[1] = [
+                    [id:"fasta"],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists:true)
+                ]
+                input[2] = [
+                    [id:"fai"],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists:true)
+                ]
+                input[3] = [
+                    [id:"dict"],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.dict', checkIfExists:true)
+                ]
+                input[4] = [
+                    [id:"dbsnp"],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz', checkIfExists:true)
+                ]
+                input[5] = [
+                    [id:"dbsnp"],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz.tbi', checkIfExists:true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    process.out.vcf.collect { [it[0], path(it[1]).vcf.variantsMD5] },
+                    process.out.tbi.collect { [it[0], file(it[1]).name] },
+                    process.out.versions
+                ).match() }
+            )
+        }
+
+    }
+
+    test("homo_sapiens - [gvcf_gz, tbi, bed, []], fasta, fai, dict, [], []") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [id:"test"],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz.tbi', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bed', checkIfExists:true),
+                    []
+                ]
+                input[1] = [
+                    [id:"fasta"],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists:true)
+                ]
+                input[2] = [
+                    [id:"fai"],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists:true)
+                ]
+                input[3] = [
+                    [id:"dict"],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.dict', checkIfExists:true)
+                ]
+                input[4] = [[],[]]
+                input[5] = [[],[]]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    process.out.vcf.collect { [it[0], path(it[1]).vcf.variantsMD5] },
+                    process.out.tbi.collect { [it[0], file(it[1]).name] },
+                    process.out.versions
+                ).match() }
+            )
+        }
+
+    }
+
+    test("homo_sapiens - [gendb, [], [], []], fasta, fai, dict, [], []") {
+
+        when {
+            process {
+                """
+                input[0] = UNTAR.out.untar.map { meta, gendb -> [ meta, gendb, [], [], []] }
+                input[1] = [
+                    [id:"fasta"],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists:true)
+                ]
+                input[2] = [
+                    [id:"fai"],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists:true)
+                ]
+                input[3] = [
+                    [id:"dict"],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.dict', checkIfExists:true)
+                ]
+                input[4] = [[],[]]
+                input[5] = [[],[]]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    process.out.vcf.collect { [it[0], path(it[1]).vcf.variantsMD5] },
+                    process.out.tbi.collect { [it[0], file(it[1]).name] },
+                    process.out.versions
+                ).match() }
+            )
+        }
+
+    }
+
+    test("homo_sapiens - [gendb, bed, [], []], fasta, fai, dict, [], []") {
+
+        when {
+            process {
+                """
+                input[0] = UNTAR.out.untar.map { meta, gendb -> 
+                    [ 
+                        meta,
+                        gendb,
+                        [],
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bed', checkIfExists:true),
+                        []
+                    ] 
+                }
+                input[1] = [
+                    [id:"fasta"],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists:true)
+                ]
+                input[2] = [
+                    [id:"fai"],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists:true)
+                ]
+                input[3] = [
+                    [id:"dict"],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.dict', checkIfExists:true)
+                ]
+                input[4] = [[],[]]
+                input[5] = [[],[]]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    process.out.vcf.collect { [it[0], path(it[1]).vcf.variantsMD5] },
+                    process.out.tbi.collect { [it[0], file(it[1]).name] },
+                    process.out.versions
+                ).match() }
+            )
+        }
+
+    }
+
+    test("homo_sapiens - [gvcf, idx, [], []], fasta, fai, dict, [], [] - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [id:"test"],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.idx', checkIfExists: true),
+                    [],
+                    []
+                ]
+                input[1] = [
+                    [id:"fasta"],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists:true)
+                ]
+                input[2] = [
+                    [id:"fai"],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists:true)
+                ]
+                input[3] = [
+                    [id:"dict"],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.dict', checkIfExists:true)
+                ]
+                input[4] = [[],[]]
+                input[5] = [[],[]]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+}