From 26311aba2ace0eda4201651abe9276dbd8c2aef0 Mon Sep 17 00:00:00 2001
From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com>
Date: Tue, 3 May 2022 15:04:37 +0200
Subject: [PATCH] fix minor errors

---
 modules/cnvpytor/callcnvs/main.nf    | 2 +-
 modules/cnvpytor/view/meta.yml       | 3 +++
 tests/modules/cnvpytor/view/test.yml | 1 +
 3 files changed, 5 insertions(+), 1 deletion(-)

diff --git a/modules/cnvpytor/callcnvs/main.nf b/modules/cnvpytor/callcnvs/main.nf
index c3866095..092f6def 100644
--- a/modules/cnvpytor/callcnvs/main.nf
+++ b/modules/cnvpytor/callcnvs/main.nf
@@ -19,7 +19,7 @@ process CNVPYTOR_CALLCNVS {
     task.ext.when == null || task.ext.when
 
     script:
-    def args = task.ext.args ?: '1000'
+    def bins = bin_sizes ?: '1000'
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
     cnvpytor \\
diff --git a/modules/cnvpytor/view/meta.yml b/modules/cnvpytor/view/meta.yml
index 0f9bbb43..1392e90e 100644
--- a/modules/cnvpytor/view/meta.yml
+++ b/modules/cnvpytor/view/meta.yml
@@ -24,6 +24,9 @@ input:
   - bin_sizes:
       type: string
       description: list of binsizes separated by space e.g. "1000 10000" and "1000"
+  - output_format:
+      type: string
+      description: output format of the cnv calls. Valid entries are "tsv", "vcf", and "xls"
 
 output:
   - meta:
diff --git a/tests/modules/cnvpytor/view/test.yml b/tests/modules/cnvpytor/view/test.yml
index 9c8b346b..ea8ab792 100644
--- a/tests/modules/cnvpytor/view/test.yml
+++ b/tests/modules/cnvpytor/view/test.yml
@@ -5,6 +5,7 @@
     - cnvpytor/view
   files:
     - path: output/cnvpytor/test_10000.vcf
+    - path: output/cnvpytor/test_100000.vcf
     - path: output/cnvpytor/versions.yml
 
 - name: cnvpytor view test_cnvpytor_view tsv