diff --git a/pytest.ini b/pytest.ini
new file mode 100644
index 0000000000000000000000000000000000000000..c8d98f29942ac24e83b741a0e102714b44230eab
--- /dev/null
+++ b/pytest.ini
@@ -0,0 +1,2 @@
+[pytest]
+python_paths = workflow/scripts
diff --git a/workflow/rna-seq.nf b/workflow/rna-seq.nf
index 940baa44123513af34bc00f464b9bb25bc849eda..0c4077ee501500129fd5d2596efbb5db48cfe63d 100755
--- a/workflow/rna-seq.nf
+++ b/workflow/rna-seq.nf
@@ -17,7 +17,7 @@ bdbag = Channel
   .ifEmpty { exit 1, "deriva cookie file for bdbag not found: ${params.bdbag}" }
 repRID = params.repRID
 outDir = params.outDir
-reference = params.reference
+referenceBase = file ("${params.reference}")
 logsDir = "${outDir}/Logs"
 
 // Define fixed files
@@ -203,7 +203,7 @@ referenceDir.into {
 */
 process trimData {
   tag "${repRID}"
-  publishDir "${logsDir}", mode: 'copy', pattern: "\${repRID}.trimData.*"
+  publishDir "${logsDir}", mode: 'copy', pattern: "${repRID}.trimData.*"
 
   input:
     val endsManual_trimData
@@ -234,7 +234,8 @@ process trimData {
 */
 process alignReads {
   tag "align-${repRID}"
-  publishDir "${outDir}/aligned", mode: "copy"
+  publishDir "${outDir}/aligned", mode: "copy", pattern: "${repRID}.{unal,sorted}.{gz,bam,bai}"
+  publishDir "${logsDir}", mode: 'copy', pattern: "${repRID}.align.{out,err}"
 
   input:
     val endsManual_alignReads
@@ -244,6 +245,7 @@ process alignReads {
 
   output:
     set repRID, file ("${repRID}.unal.gz"), file ("${repRID}.sorted.bam"), file ("${repRID}.sorted.bai")
+    set repRID, file ("${repRID}.align.out"), file ("${repRID}.align.err")
 
   script:
     """
diff --git a/workflow/tests/test_align.py b/workflow/tests/test_align.py
new file mode 100644
index 0000000000000000000000000000000000000000..dcbecebd6ce24ac96184f6fe06c24bdb9207751e
--- /dev/null
+++ b/workflow/tests/test_align.py
@@ -0,0 +1,40 @@
+#!/usr/bin/env python3
+
+import pytest
+import pandas as pd
+import os
+import utils
+
+data_output_path = os.path.dirname(os.path.abspath(__file__)) + \
+	'/../../output/aligned'
+logs_output_path = os.path.dirname(os.path.abspath(__file__)) + \
+	'/../../output/Logs'
+
+@pytest.mark.alignData
+def test_alignData_se():
+	assert os.path.exists(os.path.join(data_output_path, '16-1ZX4.unal.gz'))
+	assert utils.count_lines(os.path.join(data_output_path, '16-1ZX4.unal.gz')) == 3070504
+	assert os.path.exists(os.path.join(data_output_path, 'Q-Y5JA.sorted.bam'))
+	assert utils.count_lines(os.path.join(data_output_path, 'Q-Y5JA.sorted.bam')) == 5805611
+	assert os.path.exists(os.path.join(data_output_path, 'Q-Y5JA.sorted.bai'))
+	assert utils.count_lines(os.path.join(data_output_path, 'Q-Y5JA.sorted.bai')) == 12824
+def test_alignData_pe():
+	assert os.path.exists(os.path.join(data_output_path, 'Q-Y5JA.unal.gz'))
+	assert utils.count_lines(os.path.join(data_output_path, 'Q-Y5JA.unal.gz')) == 0
+	assert os.path.exists(os.path.join(data_output_path, 'Q-Y5JA.sorted.bam'))
+	assert utils.count_lines(os.path.join(data_output_path, 'Q-Y5JA.sorted.bam')) == 5805611
+	assert os.path.exists(os.path.join(data_output_path, 'Q-Y5JA.sorted.bai'))
+	assert utils.count_lines(os.path.join(data_output_path, 'Q-Y5JA.sorted.bai')) == 12824
+@pytest.mark.alignLogs
+def test_alignLogs_se():
+	assert os.path.exists(os.path.join(logs_output_path, '16-1ZX4.align.err'))
+	assert utils.count_lines(os.path.join(logs_output_path, '16-1ZX4.align.err')) == 7
+	assert '34497376 reads; of these:' in open(os.path.join(logs_output_path, '16-1ZX4.align.err')).readlines()[0]
+	assert os.path.exists(os.path.join(logs_output_path, '16-1ZX4.align.out'))
+	assert utils.count_lines(os.path.join(logs_output_path, '16-1ZX4.align.out')) == 0
+def test_alignLogs_pe():
+	assert os.path.exists(os.path.join(logs_output_path, 'Q-Y5JA.align.err'))
+	assert utils.count_lines(os.path.join(logs_output_path, 'Q-Y5JA.align.err')) == 7
+	assert '15824858 reads; of these:' in open(os.path.join(logs_output_path, 'Q-Y5JA.align.err')).readlines()[0]
+	assert os.path.exists(os.path.join(logs_output_path, 'Q-Y5JA.align.out'))
+	assert utils.count_lines(os.path.join(logs_output_path, 'Q-Y5JA.align.out')) == 0