From dda7cf975383ca35201af709dc577efb2153f90c Mon Sep 17 00:00:00 2001
From: s181706 <jonathan.gesell@utsouthwestern.edu>
Date: Thu, 23 Jan 2020 14:36:28 -0600
Subject: [PATCH] Added files necessary for CI of output files.
---
pytest.ini | 2 ++
workflow/rna-seq.nf | 8 +++++---
workflow/tests/test_align.py | 40 ++++++++++++++++++++++++++++++++++++
3 files changed, 47 insertions(+), 3 deletions(-)
create mode 100644 pytest.ini
create mode 100644 workflow/tests/test_align.py
diff --git a/pytest.ini b/pytest.ini
new file mode 100644
index 0000000..c8d98f2
--- /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 940baa4..0c4077e 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 0000000..dcbeceb
--- /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
--
GitLab