From f723f33b20d08e95a803691ffab562c0d11c1e0a Mon Sep 17 00:00:00 2001
From: Chang Ye <yech1990@gmail.com>
Date: Tue, 18 Jun 2024 19:17:09 -0500
Subject: [PATCH] fix json report

---
 cutseq/run.py  | 54 ++++++++++++++++++++++++++------------------------
 pyproject.toml |  2 +-
 2 files changed, 29 insertions(+), 27 deletions(-)

diff --git a/cutseq/run.py b/cutseq/run.py
index 542f840..100392d 100644
--- a/cutseq/run.py
+++ b/cutseq/run.py
@@ -427,19 +427,20 @@ def pipeline_single(input1, output1, short1, untrimmed1, barcode, settings):
         pipeline = SingleEndPipeline(modifiers, steps)
         stats = runner.run(pipeline, Progress(), outfiles)
 
-        json_report(
-            settings.json_file,
-            stats,
-            barcode,
-            input1,
-            None,
-            output1,
-            None,
-            short1,
-            None,
-            untrimmed1,
-            None,
-        )
+        if settings.json_file is not None:
+            json_report(
+                settings.json_file,
+                stats,
+                barcode,
+                input1,
+                None,
+                output1,
+                None,
+                short1,
+                None,
+                untrimmed1,
+                None,
+            )
         print(minimal_report(stats, time=None, gc_content=None), file=sys.stderr)
     outfiles.close()
 
@@ -686,19 +687,20 @@ def pipeline_paired(
         pipeline = PairedEndPipeline(modifiers, steps)
         stats = runner.run(pipeline, Progress(), outfiles)
 
-        json_report(
-            settings.json_file,
-            stats,
-            barcode,
-            input1,
-            input2,
-            output1,
-            output2,
-            short1,
-            short2,
-            untrimmed1,
-            untrimmed2,
-        )
+        if settings.json_file is not None:
+            json_report(
+                settings.json_file,
+                stats,
+                barcode,
+                input1,
+                input2,
+                output1,
+                output2,
+                short1,
+                short2,
+                untrimmed1,
+                untrimmed2,
+            )
         print(minimal_report(stats, time=None, gc_content=None), file=sys.stderr)
 
     outfiles.close()
diff --git a/pyproject.toml b/pyproject.toml
index c50bad4..d71de5c 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "cutseq"
-version = "0.0.42"
+version = "0.0.43"
 description = "Automatically cut adapter / barcode / UMI from NGS data"
 authors = ["Ye Chang <yech1990@gmail.com>"]
 license = "MIT"