From bee6bab94593c0d24f6df153341d6418c4ccfa75 Mon Sep 17 00:00:00 2001
From: meono <emoz@biosustain.dtu.dk>
Date: Wed, 20 Nov 2019 23:19:52 +0100
Subject: [PATCH] Fix: eliminate potential deadlock Add: direct bcl2fastq
 command output to files Update Dockerfile with version

---
 Dockerfile       |  2 +-
 run_container.py | 10 +++++++---
 2 files changed, 8 insertions(+), 4 deletions(-)

diff --git a/Dockerfile b/Dockerfile
index 72bc939..d56e87c 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -16,7 +16,7 @@ RUN conda install -y python=3.7.3
 RUN cd /tmp && \
     git clone https://github.com/meono/library_to_samplesheet.git && \
     cd library_to_samplesheet && \
-    git checkout v0.1.3 && \
+    git checkout v0.1.4 && \
     pip install -e .
 
 CMD python run_container.py
diff --git a/run_container.py b/run_container.py
index 56a157a..96fa681 100644
--- a/run_container.py
+++ b/run_container.py
@@ -61,12 +61,16 @@
                          '--processing-threads', '8',
                          '--loading-threads', '4',
                          '--writing-threads', '4',
-                         '1>', f'{run_path}/bcl2fastq.out',
-                         '2>', f'{run_path}/bcl2fastq.err'
                          ],
                         stdout=PIPE, stderr=PIPE)
-    process_b2f.wait()
     stdout, stderr = process_b2f.communicate()
+
+    # write stdout and strerr to files
+    with open(f'{run_path}/bcl2fastq.out', 'w') outfile:
+        outfile.writelines(stdout.decode())
+    with open(f'{run_path}/bcl2fastq.err', 'w') errfile:
+        outfile.writelines(stderr.decode())
+
     # return error message is something went wrong
     if process_b2f.returncode != 0:
         print(f'Bcl2fastq failed with return code '