From c805f165ee48a9998c918076aefdfce937f8cd26 Mon Sep 17 00:00:00 2001
From: Venkat Malladi <venkat.malladi@utsouthwestern.edu>
Date: Tue, 28 Jan 2020 11:40:46 -0600
Subject: [PATCH] Add a single control end-end test.
---
.gitlab-ci.yml | 10 ++++++++++
test_data/fetch_test_data.sh | 6 ++++++
workflow/tests/test_pool_and_psuedoreplicate.py | 1 +
3 files changed, 17 insertions(+)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 6782976..d98336b 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -8,6 +8,7 @@ stages:
- unit
- astrocyte
- single
+ - control
- multiple
- skip
@@ -45,6 +46,15 @@ paired_end_human:
- nextflow run workflow/main.nf --designFile "$CI_PROJECT_DIR/test_data/design_ENCSR729LGA_PE.txt" --genome 'GRCh38' --pairedEnd true --astrocyte false -resume
- pytest -m pairedend
+single_end_single_control:
+ stage: single
+ only:
+ - branches
+ except:
+ - master
+ script:
+ - nextflow run workflow/main.nf --designFile "$CI_PROJECT_DIR/test_data/design_single_contol_SE.txt" --genome 'GRCh38' --pairedEnd false --astrocyte false -resume
+
single_end_diff:
stage: multiple
only:
diff --git a/test_data/fetch_test_data.sh b/test_data/fetch_test_data.sh
index 8b9a331..09e30b5 100644
--- a/test_data/fetch_test_data.sh
+++ b/test_data/fetch_test_data.sh
@@ -25,3 +25,9 @@ wget https://www.encodeproject.org/files/ENCFF161HBP/@@download/ENCFF161HBP.fast
wget https://www.encodeproject.org/files/ENCFF776KZU/@@download/ENCFF776KZU.fastq.gz
wget https://www.encodeproject.org/files/ENCFF119KHM/@@download/ENCFF119KHM.fastq.gz
echo "Done with Paired-end"
+
+echo "Downloading Single-end data set Human ENCSR000DXB and ENCSR000DXC"
+wget https://www.encodeproject.org/files/ENCFF001GBW/@@download/ENCFF001GBW.fastq.gz
+wget https://www.encodeproject.org/files/ENCFF001GBV/@@download/ENCFF001GBV.fastq.gz
+wget https://www.encodeproject.org/files/ENCFF001HWJ/@@download/ENCFF001HWJ.fastq.gz
+echo "Done with Single-end"
diff --git a/workflow/tests/test_pool_and_psuedoreplicate.py b/workflow/tests/test_pool_and_psuedoreplicate.py
index f251e88..7f219c9 100644
--- a/workflow/tests/test_pool_and_psuedoreplicate.py
+++ b/workflow/tests/test_pool_and_psuedoreplicate.py
@@ -72,6 +72,7 @@ def test_single_rep(design_experiment_2):
single_rep = pool_and_psuedoreplicate.generate_design('false', 1.2, design_experiment_2, cwd, 1, 1)
assert single_rep.shape[0] == 4
+
@pytest.mark.singleend
def test_pool_and_psuedoreplicate_singleend():
design_file = os.path.join(test_output_path, 'ENCSR238SGC_ppr.tsv')
--
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