From 6e218123f98d1fbc81aaae496b0c4b2401561702 Mon Sep 17 00:00:00 2001
From: Jorisvansteenbrugge
 <7196110+Jorisvansteenbrugge@users.noreply.github.com>
Date: Wed, 8 Apr 2026 17:01:10 +0200
Subject: [PATCH] demo prs modules

---
 UMCUGenetics/pgscatalog/combine/main.nf       | 27 +++++++++
 .../pgscatalog/combine/tests/main.nf.test     | 27 +++++++++
 UMCUGenetics/pgscatalog/match/main.nf         | 42 ++++++++++++++
 .../pgscatalog/match/tests/main.nf.test       | 58 +++++++++++++++++++
 4 files changed, 154 insertions(+)
 create mode 100644 UMCUGenetics/pgscatalog/combine/main.nf
 create mode 100644 UMCUGenetics/pgscatalog/combine/tests/main.nf.test
 create mode 100644 UMCUGenetics/pgscatalog/match/main.nf
 create mode 100644 UMCUGenetics/pgscatalog/match/tests/main.nf.test

diff --git a/UMCUGenetics/pgscatalog/combine/main.nf b/UMCUGenetics/pgscatalog/combine/main.nf
new file mode 100644
index 0000000..a651c19
--- /dev/null
+++ b/UMCUGenetics/pgscatalog/combine/main.nf
@@ -0,0 +1,27 @@
+process PGSCATALOG_COMBINE {
+    tag "${meta.id}"
+
+    container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
+        ? 'https://depot.galaxyproject.org/singularity/pgscatalog-utils:1.4.4--pyhdfd78af_0'
+        : 'biocontainers/pgscatalog-utils:1.4.4--pyhdfd78af_0'}"
+
+    input:
+    tuple val(meta), path(scoring_file)
+    val assembly_version
+
+    output:
+    tuple val(meta), path("*_normalised.txt.gz"), emit: normalised_model
+    path "versions.yml", emit: versions
+
+    script:
+    def prefix = task.ext.prefix ?: meta.id
+    """
+    pgscatalog-combine \\
+        -s ${scoring_file} \\
+        -t ${assembly_version} \\
+        -o ${prefix}_normalised.txt.gz
+
+
+    echo "pgscatalog-combine: 1.4.4" > versions.yml
+    """
+}
diff --git a/UMCUGenetics/pgscatalog/combine/tests/main.nf.test b/UMCUGenetics/pgscatalog/combine/tests/main.nf.test
new file mode 100644
index 0000000..748609f
--- /dev/null
+++ b/UMCUGenetics/pgscatalog/combine/tests/main.nf.test
@@ -0,0 +1,27 @@
+nextflow_process {
+    name "Test Process PGScatalog-combine"
+    script "../main.nf"
+    process "PGSCATALOG_COMBINE"
+
+    tag "modules/local"
+
+
+    test("Test Correct model formatting "){
+        when{
+            process{
+                """
+                input[0] = [[id: 'model'],
+                    file("${projectDir}/assets/models/BCAC_313_PRS_GRCh38.txt",
+                    checkifExists: true)]
+                input[1] = channel.value("GRCh38")
+                """
+            }
+
+            then {
+                assertAll(
+                    {assert process.success},
+                )
+            }
+        }
+    }
+}
diff --git a/UMCUGenetics/pgscatalog/match/main.nf b/UMCUGenetics/pgscatalog/match/main.nf
new file mode 100644
index 0000000..8d2db1b
--- /dev/null
+++ b/UMCUGenetics/pgscatalog/match/main.nf
@@ -0,0 +1,42 @@
+process PGSCATALOG_MATCH {
+    tag "${meta.id}"
+
+    container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
+        ? 'https://depot.galaxyproject.org/singularity/pgscatalog-utils:1.4.4--pyhdfd78af_0'
+        : 'biocontainers/pgscatalog-utils:1.4.4--pyhdfd78af_0'}"
+
+    input:
+    tuple val(meta), path(pvar)
+    tuple val(meta2), path(scoring_file)
+
+
+    output:
+    tuple val(meta), path("*_summary.csv"), emit: summary
+    tuple val(meta), path("*.scorefile.gz"), emit: scorefile
+    tuple val(meta), path("*_log.csv.gz"), emit: log
+    path "versions.yml", emit: versions
+
+    script:
+    def prefix = task.ext.prefix ?: meta.id
+    def args = task.ext.args ?: ""
+    """
+    pgscatalog-match \\
+        ${args} \\
+        --dataset ${prefix} \\
+        --scorefiles ${scoring_file} \\
+        --target ${pvar} \\
+        --outdir ./
+
+    echo "pgscatalog-match: 1.4.4" > versions.yml
+    """
+
+    stub:
+    def prefix = task.ext.prefix ?: "Cohort"
+    """
+	touch ${prefix}_summary.csv
+	touch ${prefix}.scorefile.gz
+    touch ${prefix}_log.csv.gz
+
+	echo "pgscatalog-match: 1.4.4" > versions.yml
+	"""
+}
diff --git a/UMCUGenetics/pgscatalog/match/tests/main.nf.test b/UMCUGenetics/pgscatalog/match/tests/main.nf.test
new file mode 100644
index 0000000..176b6ad
--- /dev/null
+++ b/UMCUGenetics/pgscatalog/match/tests/main.nf.test
@@ -0,0 +1,58 @@
+nextflow_process {
+    name "Test Process PGScatalog-match"
+    script "../main.nf"
+    process "PGSCATALOG_MATCH"
+
+
+
+    tag "modules/local"
+
+    test("Test SNV ambiguity detection"){
+        setup{
+            run("PLINK2_VCF") {
+                script "../../../../nf-core/plink2/vcf/main.nf"
+
+                process{
+                    """
+                        input[0] = [[id: "vcf"], file("${projectDir}/assets/test-data/test.vcf",checkIfExists: true)]
+                    """
+                }
+            }
+        }
+
+        when {
+            process {
+                """
+                input[0] = [[id: "model"],
+                        file(
+                            "${projectDir}/assets/test-data/norm_test_model_subworkflow.txt.gz",
+                            checkIfExists: true)]
+                    input[1] = PLINK2_VCF.out.pvar_zst
+                    
+                """
+            }  
+        }
+        then {
+            // Analysing the csv is necessary as the snapshots do not always match
+            // (row order differs)
+            def csv = path(process.out.summary[0][1]).csv().table
+            def matched = csv.stringColumn("match_status").isEqualTo("matched")
+            
+            def n_ambiguous_SNV = csv.where(
+                csv.booleanColumn("ambiguous").isTrue().and(matched)
+            ).row(0).getInt("count")
+
+            def n_unambiguous_SNV = csv.where(
+                csv.booleanColumn("ambiguous").isFalse().and(matched)
+            ).row(0).getInt("count")
+            
+            assertAll (
+                {assert process.success},
+                {assert n_ambiguous_SNV == 1},
+                {assert n_unambiguous_SNV == 3}
+            )
+        }
+            
+    
+    }
+}