From af5ef3cd4a9529e8e1440d2203fcc8301b1877d5 Mon Sep 17 00:00:00 2001
From: lindaxiang <linda.xiang@oicr.on.ca>
Date: Tue, 12 May 2020 18:22:09 -0400
Subject: [PATCH 1/4] set pu and pi as optional parameters

---
 .../sanger-wgs-variant-caller.nf                     | 12 +++++++-----
 1 file changed, 7 insertions(+), 5 deletions(-)

diff --git a/tools/sanger-wgs-variant-caller/sanger-wgs-variant-caller.nf b/tools/sanger-wgs-variant-caller/sanger-wgs-variant-caller.nf
index cb1385d..4d5112e 100644
--- a/tools/sanger-wgs-variant-caller/sanger-wgs-variant-caller.nf
+++ b/tools/sanger-wgs-variant-caller/sanger-wgs-variant-caller.nf
@@ -23,7 +23,7 @@
  */
 
 nextflow.preview.dsl=2
-version = '2.1.0-6'
+version = '2.1.0-7'
 
 params.ref_genome_tar = ""
 params.vagrent_annot = ""
@@ -41,8 +41,8 @@ params.skipqc = false
 params.skipannot = false
 params.pindelcpu = 8
 params.cavereads = 350000
-params.purity = 1.0
-params.ploidy = 2.0
+params.purity = ""
+params.ploidy = ""
 params.container_version = ""
 params.cpus = 24
 params.mem = 128  // GB
@@ -86,6 +86,8 @@ process sangerWgsVariantCaller {
   script:
     arg_skipqc = params.skipqc ? "-skipqc" : ""
     arg_skipannot = params.skipannot ? "-skipannot" : ""
+    arg_pu = params.pu ? "-pu ${params.pu}" : ""
+    arg_pi = params.pi ? "-pu ${params.pi}" : ""
     """
     /opt/wtsi-cgp/bin/ds-cgpwgs.pl \
       -cores ${task.cpus} \
@@ -105,8 +107,8 @@ process sangerWgsVariantCaller {
       ${arg_skipannot} \
       -pindelcpu ${params.pindelcpu} \
       -cavereads ${params.cavereads} \
-      -pu ${params.purity} \
-      -pi ${params.ploidy} \
+      ${arg_pu} \
+      ${arg_pi} \
       -outdir \$PWD
     """
 }

From e7a4e8eae2e940c6a8b9d82a5e120e5d843d6d73 Mon Sep 17 00:00:00 2001
From: lindaxiang <linda.xiang@oicr.on.ca>
Date: Tue, 12 May 2020 20:09:04 -0400
Subject: [PATCH 2/4] further fix

---
 .../sanger-wgs-variant-caller/sanger-wgs-variant-caller.nf  | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/tools/sanger-wgs-variant-caller/sanger-wgs-variant-caller.nf b/tools/sanger-wgs-variant-caller/sanger-wgs-variant-caller.nf
index 4d5112e..bbd60cf 100644
--- a/tools/sanger-wgs-variant-caller/sanger-wgs-variant-caller.nf
+++ b/tools/sanger-wgs-variant-caller/sanger-wgs-variant-caller.nf
@@ -23,7 +23,7 @@
  */
 
 nextflow.preview.dsl=2
-version = '2.1.0-7'
+version = '2.1.0-8'
 
 params.ref_genome_tar = ""
 params.vagrent_annot = ""
@@ -86,8 +86,8 @@ process sangerWgsVariantCaller {
   script:
     arg_skipqc = params.skipqc ? "-skipqc" : ""
     arg_skipannot = params.skipannot ? "-skipannot" : ""
-    arg_pu = params.pu ? "-pu ${params.pu}" : ""
-    arg_pi = params.pi ? "-pu ${params.pi}" : ""
+    arg_pu = params.purity ? "-pu ${params.purity}" : ""
+    arg_pi = params.ploidy ? "-pu ${params.ploidy}" : ""
     """
     /opt/wtsi-cgp/bin/ds-cgpwgs.pl \
       -cores ${task.cpus} \

From 182e7dc27ecf4a15f4d2d9f11e9e8b322604d0f0 Mon Sep 17 00:00:00 2001
From: lindaxiang <linda.xiang@oicr.on.ca>
Date: Wed, 13 May 2020 10:53:36 -0400
Subject: [PATCH 3/4] more proper default values

---
 .../sanger-wgs-variant-caller.nf                          | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/tools/sanger-wgs-variant-caller/sanger-wgs-variant-caller.nf b/tools/sanger-wgs-variant-caller/sanger-wgs-variant-caller.nf
index bbd60cf..894236f 100644
--- a/tools/sanger-wgs-variant-caller/sanger-wgs-variant-caller.nf
+++ b/tools/sanger-wgs-variant-caller/sanger-wgs-variant-caller.nf
@@ -41,8 +41,8 @@ params.skipqc = false
 params.skipannot = false
 params.pindelcpu = 8
 params.cavereads = 350000
-params.purity = ""
-params.ploidy = ""
+params.purity = null
+params.ploidy = null
 params.container_version = ""
 params.cpus = 24
 params.mem = 128  // GB
@@ -86,8 +86,8 @@ process sangerWgsVariantCaller {
   script:
     arg_skipqc = params.skipqc ? "-skipqc" : ""
     arg_skipannot = params.skipannot ? "-skipannot" : ""
-    arg_pu = params.purity ? "-pu ${params.purity}" : ""
-    arg_pi = params.ploidy ? "-pu ${params.ploidy}" : ""
+    arg_pu = (params.purity!=null) ? "-pu ${params.purity}" : ""
+    arg_pi = (params.ploidy!=null) ? "-pi ${params.ploidy}" : ""
     """
     /opt/wtsi-cgp/bin/ds-cgpwgs.pl \
       -cores ${task.cpus} \

From 30811fe120ffa86f11b4c7164c0d5a55f5d4c323 Mon Sep 17 00:00:00 2001
From: lindaxiang <linda.xiang@oicr.on.ca>
Date: Wed, 13 May 2020 10:55:42 -0400
Subject: [PATCH 4/4] bump version

---
 tools/sanger-wgs-variant-caller/sanger-wgs-variant-caller.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tools/sanger-wgs-variant-caller/sanger-wgs-variant-caller.nf b/tools/sanger-wgs-variant-caller/sanger-wgs-variant-caller.nf
index 894236f..0c14d0d 100644
--- a/tools/sanger-wgs-variant-caller/sanger-wgs-variant-caller.nf
+++ b/tools/sanger-wgs-variant-caller/sanger-wgs-variant-caller.nf
@@ -23,7 +23,7 @@
  */
 
 nextflow.preview.dsl=2
-version = '2.1.0-8'
+version = '2.1.0-9'
 
 params.ref_genome_tar = ""
 params.vagrent_annot = ""