From a6cb75174bfbd131f3da14d8cd3e34c1a2e6e268 Mon Sep 17 00:00:00 2001
From: Anders Jemt <jemten@users.noreply.github.com>
Date: Tue, 19 Apr 2022 10:53:39 +0200
Subject: [PATCH] Add variant catalog ch to stranger (#1508)

* Add optional variant catalog input

* fix for no variant catalog test

Co-authored-by: ljmesi <37740329+ljmesi@users.noreply.github.com>
Co-authored-by: Lauri Mesilaakso <john.mesilaakso@gmail.com>
---
 modules/stranger/main.nf        |  5 ++++-
 modules/stranger/meta.yml       |  4 ++++
 tests/modules/stranger/main.nf  | 24 +++++++++++++++---------
 tests/modules/stranger/test.yml | 16 +++++++++++++++-
 4 files changed, 38 insertions(+), 11 deletions(-)

diff --git a/modules/stranger/main.nf b/modules/stranger/main.nf
index 2e647627..55678bd3 100644
--- a/modules/stranger/main.nf
+++ b/modules/stranger/main.nf
@@ -9,6 +9,7 @@ process STRANGER {
 
     input:
     tuple val(meta), path(vcf)
+    path variant_catalog
 
     output:
     tuple val(meta), path("*.gz"), emit: vcf
@@ -20,10 +21,12 @@ process STRANGER {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
+    def options_variant_catalog = variant_catalog ? "--repeats-file $variant_catalog" : ""
     """
     stranger \\
         $args \\
-        $vcf | gzip --no-name > ${prefix}.vcf.gz
+        $vcf \\
+        $options_variant_catalog | gzip --no-name > ${prefix}.vcf.gz
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/stranger/meta.yml b/modules/stranger/meta.yml
index 61ebc7a9..0707d806 100644
--- a/modules/stranger/meta.yml
+++ b/modules/stranger/meta.yml
@@ -24,6 +24,10 @@ input:
       type: file
       description: VCF with repeat expansions
       pattern: "*.{vcf.gz,vcf}"
+  - variant_catalog:
+      type: file
+      description: json file with repeat expansion sites to genotype
+      pattern: "*.{json}"
 
 output:
   - meta:
diff --git a/tests/modules/stranger/main.nf b/tests/modules/stranger/main.nf
index bc4bd3ce..5bd6766b 100644
--- a/tests/modules/stranger/main.nf
+++ b/tests/modules/stranger/main.nf
@@ -5,15 +5,21 @@ nextflow.enable.dsl = 2
 include { EXPANSIONHUNTER } from '../../../modules/expansionhunter/main.nf'
 include { STRANGER } from '../../../modules/stranger/main.nf'
 
+
+input = [ [ id:'test', gender:'male' ], // meta map
+            file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
+            file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
+        ]
+fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+variant_catalog = file(params.test_data['homo_sapiens']['genome']['repeat_expansions'], checkIfExists: true)
+
+
 workflow test_stranger {
-
-    input = [ [ id:'test', gender:'male' ], // meta map
-              file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
-              file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
-            ]
-    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
-    variant_catalog = file(params.test_data['homo_sapiens']['genome']['repeat_expansions'], checkIfExists: true)
-
     EXPANSIONHUNTER ( input, fasta, variant_catalog )
-    STRANGER ( EXPANSIONHUNTER.out.vcf )
+    STRANGER ( EXPANSIONHUNTER.out.vcf, variant_catalog )
+}
+
+workflow test_stranger_without_optional_variant_catalog {
+    EXPANSIONHUNTER ( input, fasta, variant_catalog )
+    STRANGER ( EXPANSIONHUNTER.out.vcf, [] )
 }
diff --git a/tests/modules/stranger/test.yml b/tests/modules/stranger/test.yml
index 821928e8..c7a6972e 100644
--- a/tests/modules/stranger/test.yml
+++ b/tests/modules/stranger/test.yml
@@ -8,6 +8,20 @@
     - path: output/expansionhunter/versions.yml
       md5sum: f3962a6eecfddf9682414c0f605a885a
     - path: output/stranger/test.vcf.gz
-      md5sum: bbe15159195681d5c18596d3ad85c78f
+      md5sum: 68b0ca1319851134ffa8793a4704dc11
     - path: output/stranger/versions.yml
       md5sum: 5ec35fd835fb1be50bc3e7c004310fc0
+
+- name: stranger test_stranger_without_optional_variant_catalog
+  command: nextflow run tests/modules/stranger -entry test_stranger_without_optional_variant_catalog -c tests/config/nextflow.config
+  tags:
+    - stranger
+  files:
+    - path: output/expansionhunter/test.vcf
+      md5sum: cfd4a1d35c0e469b99eb6aaa6d22de76
+    - path: output/expansionhunter/versions.yml
+      md5sum: c95af9e6d8cd9bd2ce1090ca4e7a6020
+    - path: output/stranger/test.vcf.gz
+      md5sum: bbe15159195681d5c18596d3ad85c78f
+    - path: output/stranger/versions.yml
+      md5sum: 8558542a007e90ea5dcdceed3f12585d