From df3d4788c4f61dcd3b59b5c68ee2142b8abc4d36 Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Tue, 29 Dec 2020 00:33:45 -0600
Subject: [PATCH] Update all tests with new test data rep
---
.gitlab-ci.yml | 2 +-
workflow/tests/test_alignReads.py | 12 ++++++------
workflow/tests/test_dataQC.py | 4 ++--
workflow/tests/test_dedupReads.py | 16 ++++++++--------
workflow/tests/test_fastqc.py | 2 +-
workflow/tests/test_getBag.py | 2 +-
workflow/tests/test_getData.py | 4 ++--
workflow/tests/test_inferMetadata.py | 2 +-
workflow/tests/test_makeBigWig.py | 2 +-
workflow/tests/test_makeFeatureCounts.py | 6 +++---
workflow/tests/test_trimData.py | 6 +++---
11 files changed, 29 insertions(+), 29 deletions(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 3047686..88100cc 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -156,7 +156,7 @@ alignData:
- singularity run 'docker://gudmaprbk/hisat2.2.1:1.0.0' samtools view -1 -@ 20 -F 4 -F 8 -F 256 -o 16-WJRA_1M.se.bam 16-WJRA_1M.se.sam
- singularity run 'docker://gudmaprbk/hisat2.2.1:1.0.0' samtools sort -@ 20 -O BAM -o 16-WJRA_1M.se.sorted.bam 16-WJRA_1M.se.bam
- singularity run 'docker://gudmaprbk/hisat2.2.1:1.0.0' samtools index -@ 20 -b 16-WJRA_1M.se.sorted.bam 16-WJRA_1M.se.sorted.bam.bai
- - singularity run 'docker://gudmaprbk/hisat2.2.1:1.0.0' hisat2 -p 20 --add-chrname --un-gz 16-WJRA_1M.pe.unal.gz -S 16-WJRA_1M.pe.sam -x /project/BICF/BICF_Core/shared/gudmap/references/GRCh38.p12.v31/hisat2/genome --rna-strandness FR --no-mixed --no-discordant -1 ./test_data/fastq/small/16-WJRA_1M.pe_R1_val_1.fq.gz -2 ./test_data/fastq/small/16-WJRA_1M.pe_R2_val_2.fq.gz --summary-file 16-WJRA_1M.pe.alignSummary.txt --new-summary
+ - singularity run 'docker://gudmaprbk/hisat2.2.1:1.0.0' hisat2 -p 20 --add-chrname --un-gz 16-WJRA_1M.pe.unal.gz -S 16-WJRA_1M.pe.sam -x /project/BICF/BICF_Core/shared/gudmap/references/GRCh38.p12.v31/hisat2/genome --rna-strandness FR --no-mixed --no-discordant -1 ./test_data/fastq/small/16-WJRA_1M.pe_val_1.fq.gz -2 ./test_data/fastq/small/16-WJRA_1M.pe_val_2.fq.gz --summary-file 16-WJRA_1M.pe.alignSummary.txt --new-summary
- singularity run 'docker://gudmaprbk/hisat2.2.1:1.0.0' samtools view -1 -@ 20 -F 4 -F 8 -F 256 -o 16-WJRA_1M.pe.bam 16-WJRA_1M.pe.sam
- singularity run 'docker://gudmaprbk/hisat2.2.1:1.0.0' samtools sort -@ 20 -O BAM -o 16-WJRA_1M.pe.sorted.bam 16-WJRA_1M.pe.bam
- singularity run 'docker://gudmaprbk/hisat2.2.1:1.0.0' samtools index -@ 20 -b 16-WJRA_1M.pe.sorted.bam 16-WJRA_1M.pe.sorted.bam.bai
diff --git a/workflow/tests/test_alignReads.py b/workflow/tests/test_alignReads.py
index 11f0f3d..d124205 100644
--- a/workflow/tests/test_alignReads.py
+++ b/workflow/tests/test_alignReads.py
@@ -12,18 +12,18 @@ data_output_path = os.path.dirname(os.path.abspath(__file__)) + \
@pytest.mark.alignData
def test_alignData_se():
assert os.path.exists(os.path.join(
- data_output_path, 'Q-Y5F6_1M.se.unal.gz'))
+ data_output_path, '16-WJRA_1M.se.unal.gz'))
assert os.path.exists(os.path.join(
- data_output_path, 'Q-Y5F6_1M.se.sorted.bam'))
+ data_output_path, '16-WJRA_1M.se.sorted.bam'))
assert os.path.exists(os.path.join(
- data_output_path, 'Q-Y5F6_1M.se.sorted.bam.bai'))
+ data_output_path, '16-WJRA_1M.se.sorted.bam.bai'))
@pytest.mark.alignData
def test_alignData_pe():
assert os.path.exists(os.path.join(
- data_output_path, 'Q-Y5F6_1M.pe.unal.gz'))
+ data_output_path, '16-WJRA_1M.pe.unal.gz'))
assert os.path.exists(os.path.join(
- data_output_path, 'Q-Y5F6_1M.pe.sorted.bam'))
+ data_output_path, '16-WJRA_1M.pe.sorted.bam'))
assert os.path.exists(os.path.join(
- data_output_path, 'Q-Y5F6_1M.pe.sorted.bam.bai'))
+ data_output_path, '16-WJRA_1M.pe.sorted.bam.bai'))
diff --git a/workflow/tests/test_dataQC.py b/workflow/tests/test_dataQC.py
index 55df66d..072253a 100644
--- a/workflow/tests/test_dataQC.py
+++ b/workflow/tests/test_dataQC.py
@@ -12,9 +12,9 @@ test_output_path = os.path.dirname(os.path.abspath(__file__)) + \
@pytest.mark.dataQC
def test_dataQC():
assert os.path.exists(os.path.join(
- test_output_path, 'Q-Y5F6_1M.se.sorted.deduped.tin.xls'))
+ test_output_path, '16-WJRA_1M.se.sorted.deduped.tin.xls'))
assert countLines(os.path.join(test_output_path,
- 'Q-Y5F6_1M.se.sorted.deduped.tin.xls'))
+ '16-WJRA_1M.se.sorted.deduped.tin.xls'))
def countLines(fileName):
diff --git a/workflow/tests/test_dedupReads.py b/workflow/tests/test_dedupReads.py
index 89fc2b1..dee270c 100644
--- a/workflow/tests/test_dedupReads.py
+++ b/workflow/tests/test_dedupReads.py
@@ -12,18 +12,18 @@ data_output_path = os.path.dirname(os.path.abspath(__file__)) + \
@pytest.mark.dedupData
def test_dedupData():
assert os.path.exists(os.path.join(
- data_output_path, 'Q-Y5F6_1M.se.sorted.deduped.bam'))
+ data_output_path, '16-WJRA_1M.se.sorted.deduped.bam'))
assert os.path.exists(os.path.join(
- data_output_path, 'Q-Y5F6_1M.se.sorted.deduped.bam.bai'))
+ data_output_path, '16-WJRA_1M.se.sorted.deduped.bam.bai'))
assert os.path.exists(os.path.join(
- data_output_path, 'Q-Y5F6_1M.se.sorted.deduped.chr8.bam'))
+ data_output_path, '16-WJRA_1M.se.sorted.deduped.chr8.bam'))
assert os.path.exists(os.path.join(
- data_output_path, 'Q-Y5F6_1M.se.sorted.deduped.chr8.bam.bai'))
+ data_output_path, '16-WJRA_1M.se.sorted.deduped.chr8.bam.bai'))
assert os.path.exists(os.path.join(
- data_output_path, 'Q-Y5F6_1M.se.sorted.deduped.chr4.bam'))
+ data_output_path, '16-WJRA_1M.se.sorted.deduped.chr4.bam'))
assert os.path.exists(os.path.join(
- data_output_path, 'Q-Y5F6_1M.se.sorted.deduped.chr4.bam.bai'))
+ data_output_path, '16-WJRA_1M.se.sorted.deduped.chr4.bam.bai'))
assert os.path.exists(os.path.join(
- data_output_path, 'Q-Y5F6_1M.se.sorted.deduped.chrY.bam'))
+ data_output_path, '16-WJRA_1M.se.sorted.deduped.chrY.bam'))
assert os.path.exists(os.path.join(
- data_output_path, 'Q-Y5F6_1M.se.sorted.deduped.chrY.bam.bai'))
+ data_output_path, '16-WJRA_1M.se.sorted.deduped.chrY.bam.bai'))
diff --git a/workflow/tests/test_fastqc.py b/workflow/tests/test_fastqc.py
index 07e7610..5a22a1b 100644
--- a/workflow/tests/test_fastqc.py
+++ b/workflow/tests/test_fastqc.py
@@ -12,4 +12,4 @@ test_output_path = os.path.dirname(os.path.abspath(__file__)) + \
@pytest.mark.fastqc
def test_fastqc():
assert os.path.exists(os.path.join(
- test_output_path, 'Q-Y5F6_1M.R1_fastqc.zip'))
+ test_output_path, '16-WJRA_1M.R1_fastqc.zip'))
diff --git a/workflow/tests/test_getBag.py b/workflow/tests/test_getBag.py
index 23bfc0e..66f233a 100644
--- a/workflow/tests/test_getBag.py
+++ b/workflow/tests/test_getBag.py
@@ -12,4 +12,4 @@ test_output_path = os.path.dirname(os.path.abspath(__file__)) + \
@pytest.mark.getBag
def test_getBag():
assert os.path.exists(os.path.join(
- test_output_path, 'Q-Y5F6_inputBag.zip'))
+ test_output_path, '16-WJRA_inputBag.zip'))
diff --git a/workflow/tests/test_getData.py b/workflow/tests/test_getData.py
index 596a120..926f6f9 100644
--- a/workflow/tests/test_getData.py
+++ b/workflow/tests/test_getData.py
@@ -12,6 +12,6 @@ test_output_path = os.path.dirname(os.path.abspath(__file__)) + \
@pytest.mark.getData
def test_getData():
assert os.path.exists(os.path.join(
- test_output_path, 'Q-Y5F6_inputBag/bagit.txt'))
+ test_output_path, '16-WJRA_inputBag/bagit.txt'))
assert os.path.exists(os.path.join(
- test_output_path, 'Q-Y5F6_inputBag/data/assets/Study/Q-Y4GY/Experiment/Q-Y4DP/Replicate/Q-Y5F6/mMARIS_Six2-#3.gene.rpkm.txt'))
+ test_output_path, '16-WJRA_inputBag/data/assets/Study/Q-Y4GY/Experiment/Q-Y4DP/Replicate/16-WJRA/mMARIS_Six2-#3.gene.rpkm.txt'))
diff --git a/workflow/tests/test_inferMetadata.py b/workflow/tests/test_inferMetadata.py
index 7485163..1df1d29 100644
--- a/workflow/tests/test_inferMetadata.py
+++ b/workflow/tests/test_inferMetadata.py
@@ -12,4 +12,4 @@ test_output_path = os.path.dirname(os.path.abspath(__file__)) + \
@pytest.mark.inferMetadata
def test_inferMetadata():
assert os.path.exists(os.path.join(
- test_output_path, 'Q-Y5F6_1M.se.inferMetadata.log'))
+ test_output_path, '16-WJRA_1M.se.inferMetadata.log'))
diff --git a/workflow/tests/test_makeBigWig.py b/workflow/tests/test_makeBigWig.py
index d8f62f5..35492e8 100644
--- a/workflow/tests/test_makeBigWig.py
+++ b/workflow/tests/test_makeBigWig.py
@@ -11,4 +11,4 @@ data_output_path = os.path.dirname(os.path.abspath(__file__)) + \
@pytest.mark.makeBigWig
def test_makeBigWig():
- assert os.path.exists(os.path.join(data_output_path, 'Q-Y5F6_1M.se.bw'))
+ assert os.path.exists(os.path.join(data_output_path, '16-WJRA_1M.se.bw'))
diff --git a/workflow/tests/test_makeFeatureCounts.py b/workflow/tests/test_makeFeatureCounts.py
index f6373b9..431d992 100644
--- a/workflow/tests/test_makeFeatureCounts.py
+++ b/workflow/tests/test_makeFeatureCounts.py
@@ -12,8 +12,8 @@ data_output_path = os.path.dirname(os.path.abspath(__file__)) + \
@pytest.mark.makeFeatureCounts
def test_makeFeatureCounts():
assert os.path.exists(os.path.join(
- data_output_path, 'Q-Y5F6_1M.se.countData'))
+ data_output_path, '16-WJRA_1M.se.countData'))
assert os.path.exists(os.path.join(
- data_output_path, 'Q-Y5F6_1M.se.countTable.csv'))
+ data_output_path, '16-WJRA_1M.se.countTable.csv'))
assert os.path.exists(os.path.join(
- data_output_path, 'Q-Y5F6_1M.se_tpmTable.csv'))
+ data_output_path, '16-WJRA_1M.se_tpmTable.csv'))
diff --git a/workflow/tests/test_trimData.py b/workflow/tests/test_trimData.py
index a0938e7..661663e 100644
--- a/workflow/tests/test_trimData.py
+++ b/workflow/tests/test_trimData.py
@@ -12,12 +12,12 @@ test_output_path = os.path.dirname(os.path.abspath(__file__)) + \
@pytest.mark.trimData
def test_trimData_se():
assert os.path.exists(os.path.join(
- test_output_path, 'Q-Y5F6_1M.se_trimmed.fq.gz'))
+ test_output_path, '16-WJRA_1M.se_trimmed.fq.gz'))
@pytest.mark.trimData
def test_trimData_pe():
assert os.path.exists(os.path.join(
- test_output_path, 'Q-Y5F6_1M.pe_val_1.fq.gz'))
+ test_output_path, '16-WJRA_1M.pe_val_1.fq.gz'))
assert os.path.exists(os.path.join(
- test_output_path, 'Q-Y5F6_1M.pe_val_2.fq.gz'))
+ test_output_path, '16-WJRA_1M.pe_val_2.fq.gz'))
--
GitLab