Update all tests with new test data rep

.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

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'))

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):

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'))

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'))

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'))

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'))

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'))

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'))

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'))

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'))