From 829c15c98b1447f9445690e29f2b684dbe053f65 Mon Sep 17 00:00:00 2001
From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com>
Date: Tue, 3 May 2022 14:26:34 +0200
Subject: [PATCH] partition

---
 modules/cnvpytor/partition/main.nf  | 7 ++++---
 modules/cnvpytor/partition/meta.yml | 3 +++
 2 files changed, 7 insertions(+), 3 deletions(-)

diff --git a/modules/cnvpytor/partition/main.nf b/modules/cnvpytor/partition/main.nf
index 8365cb29..42a5ec78 100644
--- a/modules/cnvpytor/partition/main.nf
+++ b/modules/cnvpytor/partition/main.nf
@@ -9,6 +9,7 @@ process CNVPYTOR_PARTITION {
 
     input:
     tuple val(meta), path(pytor)
+    val bin_sizes
 
     output:
     tuple val(meta), path("${pytor.baseName}.pytor"), emit: pytor
@@ -18,15 +19,15 @@ process CNVPYTOR_PARTITION {
     task.ext.when == null || task.ext.when
 
     script:
-    def args = task.ext.args ?: ''
+    def bins = bin_sizes ?: '1000'
     """
     cnvpytor \\
         -root $pytor \\
-        -partition $args
+        -partition $bins
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        cnvpytor: \$(echo \$(cnvpytor --version 2>&1) | sed 's/^.*pyCNVnator //; s/Using.*\$//' ))
+        cnvpytor: \$(echo \$(cnvpytor --version 2>&1) | sed 's/CNVpytor //' ))
     END_VERSIONS
     """
 
diff --git a/modules/cnvpytor/partition/meta.yml b/modules/cnvpytor/partition/meta.yml
index a72cea4c..bb7a047e 100644
--- a/modules/cnvpytor/partition/meta.yml
+++ b/modules/cnvpytor/partition/meta.yml
@@ -22,6 +22,9 @@ input:
       type: file
       description: pytor file containing read depth data
       pattern: "*.{pytor}"
+  - bin_sizes:
+      type: string
+      description: list of binsizes separated by space e.g. "1000 10000" and "1000"
 
 output:
   - meta: