Fix: eliminate potential deadlock

Add: direct bcl2fastq command output to files
Update Dockerfile with version

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

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 '