From 0eacd5547830ad1f9f1b84fcf7aa81baf597837c Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Fri, 8 Nov 2019 09:57:34 -0600
Subject: [PATCH] Remove unnecessary intermediate outputs from publish and
remove unit tests for them
---
workflow/main.nf | 4 +---
workflow/tests/test_check_design.py | 31 -------------------------
workflow/tests/test_versions.py | 35 -----------------------------
3 files changed, 1 insertion(+), 69 deletions(-)
delete mode 100644 workflow/tests/test_check_design.py
delete mode 100644 workflow/tests/test_versions.py
diff --git a/workflow/main.nf b/workflow/main.nf
index 3784116..acd7d53 100755
--- a/workflow/main.nf
+++ b/workflow/main.nf
@@ -73,7 +73,6 @@ references = params.references
process checkDesignFile {
tag "${name}"
- publishDir "${outDir}/misc/${task.process}/${name}", mode: 'copy'
module 'python/3.6.1-2-anaconda'
input:
@@ -309,7 +308,6 @@ process count310 {
process versions {
tag "${name}"
- publishDir "${outDir}/misc/${task.process}/${name}", mode: 'copy'
module 'python/3.6.1-2-anaconda:pandoc/2.7:multiqc/1.7'
input:
@@ -357,4 +355,4 @@ process multiqc {
multiqc -c ${multiqcConf} .
"""
-}
+}
\ No newline at end of file
diff --git a/workflow/tests/test_check_design.py b/workflow/tests/test_check_design.py
deleted file mode 100644
index f425d09..0000000
--- a/workflow/tests/test_check_design.py
+++ /dev/null
@@ -1,31 +0,0 @@
-#!/usr/bin/env python3
-#test_check_design.py
-#*
-#* --------------------------------------------------------------------------
-#* Licensed under MIT (https://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/blob/develop/LICENSE)
-#* --------------------------------------------------------------------------
-#*
-
-import pytest
-import pandas as pd
-from io import StringIO
-import os
-
-test_output_path = os.path.dirname(os.path.abspath(__file__)) + \
- '/../output/misc/checkDesignFile/run/'
-
-@pytest.mark.count211
-def test_count211_design():
- assert os.path.exists(os.path.join(test_output_path, 'design.checked.csv'))
-
-@pytest.mark.count301
-def test_count301_design():
- assert os.path.exists(os.path.join(test_output_path, 'design.checked.csv'))
-
-@pytest.mark.count302
-def test_count302_design():
- assert os.path.exists(os.path.join(test_output_path, 'design.checked.csv'))
-
-@pytest.mark.count310
-def test_count310_design():
- assert os.path.exists(os.path.join(test_output_path, 'design.checked.csv'))
\ No newline at end of file
diff --git a/workflow/tests/test_versions.py b/workflow/tests/test_versions.py
deleted file mode 100644
index 535e029..0000000
--- a/workflow/tests/test_versions.py
+++ /dev/null
@@ -1,35 +0,0 @@
-#!/usr/bin/env python3
-#test_versions.py
-#*
-#* --------------------------------------------------------------------------
-#* Licensed under MIT (https://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/blob/develop/LICENSE)
-#* --------------------------------------------------------------------------
-#*
-
-import pytest
-import pandas as pd
-from io import StringIO
-import os
-
-test_output_path = os.path.dirname(os.path.abspath(__file__)) + \
- '/../output/misc/versions/run/'
-
-@pytest.mark.count211
-def test_count211_versions():
- assert os.path.exists(os.path.join(test_output_path, 'versions_mqc.yaml'))
- assert os.path.exists(os.path.join(test_output_path, 'references_mqc.yaml'))
-
-@pytest.mark.count301
-def test_count301_versions():
- assert os.path.exists(os.path.join(test_output_path, 'versions_mqc.yaml'))
- assert os.path.exists(os.path.join(test_output_path, 'references_mqc.yaml'))
-
-@pytest.mark.count302
-def test_count302_versions():
- assert os.path.exists(os.path.join(test_output_path, 'versions_mqc.yaml'))
- assert os.path.exists(os.path.join(test_output_path, 'references_mqc.yaml'))
-
-@pytest.mark.count310
-def test_count310_versions():
- assert os.path.exists(os.path.join(test_output_path, 'versions_mqc.yaml'))
- assert os.path.exists(os.path.join(test_output_path, 'references_mqc.yaml'))
\ No newline at end of file
--
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