From 07e026054a018139da73534acacfdcaf8762173e Mon Sep 17 00:00:00 2001
From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com>
Date: Tue, 3 May 2022 14:24:54 +0200
Subject: [PATCH] histogram

---
 modules/cnvpytor/histogram/main.nf  | 8 +++++---
 modules/cnvpytor/histogram/meta.yml | 3 +++
 2 files changed, 8 insertions(+), 3 deletions(-)

diff --git a/modules/cnvpytor/histogram/main.nf b/modules/cnvpytor/histogram/main.nf
index f6e9dd25..1906fa36 100644
--- a/modules/cnvpytor/histogram/main.nf
+++ b/modules/cnvpytor/histogram/main.nf
@@ -9,6 +9,8 @@ process CNVPYTOR_HISTOGRAM {
 
     input:
     tuple val(meta), path(pytor)
+    val bin_sizes
+
 
     output:
     tuple val(meta), path("${pytor.baseName}.pytor")	, emit: pytor
@@ -18,15 +20,15 @@ process CNVPYTOR_HISTOGRAM {
     task.ext.when == null || task.ext.when
 
     script:
-    def args = task.ext.args ?: '1000'
+    def bins = bin_sizes ?: '1000'
     """
     cnvpytor \\
         -root $pytor \\
-        -his $args
+        -his $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/histogram/meta.yml b/modules/cnvpytor/histogram/meta.yml
index fcad2221..4855f26d 100644
--- a/modules/cnvpytor/histogram/meta.yml
+++ b/modules/cnvpytor/histogram/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: