Update CI unit tests to use repRID Q-Y5F6

.gitlab-ci.yml

@@ -15,15 +15,15 @@ getBag:
   stage: unit
   script:
   - ln -sfn `readlink -e ./test_data/auth/credential.json` ~/.deriva/credential.json
-  - singularity run 'docker://bicf/gudmaprbkfilexfer:1.3' deriva-download-cli dev.gudmap.org --catalog 2 ./workflow/conf/replicate_export_config.json . rid=16-1ZX4
+  - singularity run 'docker://bicf/gudmaprbkfilexfer:1.3' deriva-download-cli dev.gudmap.org --catalog 2 ./workflow/conf/replicate_export_config.json . rid=Q-Y5F6
   - pytest -m getBag
 
 getData:
   stage: unit
   script:
   - ln -sfn `readlink -e ./test_data/auth/cookies.txt` ~/.bdbag/deriva-cookies.txt
-  - unzip ./test_data/bagit/Study_Q-Y4H0.zip
-  - singularity run 'docker://bicf/gudmaprbkfilexfer:1.3' bash ./workflow/scripts/bdbagFetch.sh Study_Q-Y4H0 Q-Y4H0 TEST
+  - unzip ./test_data/bagit/Replicate_Q-Y5F6.zip
+  - singularity run 'docker://bicf/gudmaprbkfilexfer:1.3' bash ./workflow/scripts/bdbagFetch.sh Replicate_Q-Y5F6 Replicate_Q-Y5F6 TEST
   - pytest -m getData
 
 parseMetadata:
@@ -42,11 +42,11 @@ inferMetadata:
   stage: unit
   script:
   - >
-    align=$(echo $(grep "Overall alignment rate" ./test_data/meta/Q-Y5JA_1M.se.alignSummary.txt | cut -f2 -d ':' | cut -f2 -d ' ' | tr -d '%')) &&
+    align=$(echo $(grep "Overall alignment rate" ./test_data/meta/Q-Y5F6_1M.se.alignSummary.txt | cut -f2 -d ':' | cut -f2 -d ' ' | tr -d '%')) &&
     if [[ ${align} == "" ]]; then exit 1; fi
   - >
-    singularity run 'docker://bicf/rseqc3.0:2.0.0' infer_experiment.py -r "/project/BICF/BICF_Core/shared/gudmap/references/GRCh38.p12.v31/bed/genome.bed" -i "./test_data/bam/small/Q-Y5JA_1M.se.sorted.deduped.bam" 1>> Q-Y5JA_1M.se.inferMetadata.log &&
-    ended=`singularity run 'docker://bicf/python3:1.3' python3 ./workflow/scripts/inferMeta.sh endness Q-Y5JA_1M.se.inferMetadata.log` &&
+    singularity run 'docker://bicf/rseqc3.0:2.0.0' infer_experiment.py -r "/project/BICF/BICF_Core/shared/gudmap/references/GRCh38.p12.v31/bed/genome.bed" -i "./test_data/bam/small/Q-Y5F6_1M.se.sorted.deduped.bam" 1>> Q-Y5F6_1M.se.inferMetadata.log &&
+    ended=`singularity run 'docker://bicf/python3:1.3' python3 ./workflow/scripts/inferMeta.sh endness Q-Y5F6_1M.se.inferMetadata.log` &&
     if [[ ${ended} == "" ]]; then exit 1; fi
   - pytest -m inferMetadata
 
@@ -61,66 +61,66 @@ getRef:
 trimData:
   stage: unit
   script:
-  - singularity run 'docker://bicf/trimgalore:1.1' trim_galore --gzip -q 25 --illumina --length 35 --basename Q-Y5JA_1M.se -j 20 ./test_data/fastq/small/Q-Y5JA_1M.R1.fastq.gz
-  - singularity run 'docker://bicf/trimgalore:1.1' trim_galore --gzip -q 25 --illumina --length 35 --paired --basename Q-Y5JA_1M.pe -j 20 ./test_data/fastq/small/Q-Y5JA_1M.R1.fastq.gz ./test_data/fastq/small/Q-Y5JA_1M.R2.fastq.gz
+  - singularity run 'docker://bicf/trimgalore:1.1' trim_galore --gzip -q 25 --illumina --length 35 --basename Q-Y5F6_1M.se -j 20 ./test_data/fastq/small/Q-Y5F6_1M.R1.fastq.gz
+  - singularity run 'docker://bicf/trimgalore:1.1' trim_galore --gzip -q 25 --illumina --length 35 --paired --basename Q-Y5F6_1M.pe -j 20 ./test_data/fastq/small/Q-Y5F6_1M.R1.fastq.gz ./test_data/fastq/small/Q-Y5F6_1M.R2.fastq.gz
   - pytest -m trimData
 
 downsampleData:
   stage: unit
   script:
-  - singularity exec 'docker://bicf/seqtk:2.0.0' seqtk sample -s100 ./test_data/fastq/small/Q-Y5JA_1M_trimmed.fq.gz 1000 1> sampled.1.fq
+  - singularity exec 'docker://bicf/seqtk:2.0.0' seqtk sample -s100 ./test_data/fastq/small/Q-Y5F6_1M_trimmed.fq.gz 1000 1> sampled.1.fq
   - pytest -m downsampleData
 
 alignData:
   stage: unit
   script:
-  - singularity run 'docker://bicf/gudmaprbkaligner:2.0.0' hisat2 -p 20 --add-chrname --un-gz Q-Y5JA_1M.se.unal.gz -S Q-Y5JA_1M.se.sam -x /project/BICF/BICF_Core/shared/gudmap/references/GRCh38.p12.v31/hisat2/genome --rna-strandness F -U ./test_data/fastq/small/Q-Y5JA_1M_trimmed.fq.gz --summary-file Q-Y5JA_1M.se.alignSummary.txt --new-summary
-  - singularity run 'docker://bicf/gudmaprbkaligner:2.0.0' samtools view -1 -@ 20 -F 4 -F 8 -F 256 -o Q-Y5JA_1M.se.bam Q-Y5JA_1M.se.sam
-  - singularity run 'docker://bicf/gudmaprbkaligner:2.0.0' samtools sort -@ 20 -O BAM -o Q-Y5JA_1M.se.sorted.bam Q-Y5JA_1M.se.bam
-  - singularity run 'docker://bicf/gudmaprbkaligner:2.0.0' samtools index -@ 20 -b Q-Y5JA_1M.se.sorted.bam Q-Y5JA_1M.se.sorted.bam.bai
-  - singularity run 'docker://bicf/gudmaprbkaligner:2.0.0' hisat2 -p 20 --add-chrname --un-gz Q-Y5JA_1M.pe.unal.gz -S Q-Y5JA_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/Q-Y5JA_1M_R1_val_1.fq.gz -2 ./test_data/fastq/small/Q-Y5JA_1M_R2_val_2.fq.gz --summary-file Q-Y5JA_1M.pe.alignSummary.txt --new-summary
-  - singularity run 'docker://bicf/gudmaprbkaligner:2.0.0' samtools view -1 -@ 20 -F 4 -F 8 -F 256 -o Q-Y5JA_1M.pe.bam Q-Y5JA_1M.pe.sam
-  - singularity run 'docker://bicf/gudmaprbkaligner:2.0.0' samtools sort -@ 20 -O BAM -o Q-Y5JA_1M.pe.sorted.bam Q-Y5JA_1M.pe.bam
-  - singularity run 'docker://bicf/gudmaprbkaligner:2.0.0' samtools index -@ 20 -b Q-Y5JA_1M.pe.sorted.bam Q-Y5JA_1M.pe.sorted.bam.bai
+  - singularity run 'docker://bicf/gudmaprbkaligner:2.0.0' hisat2 -p 20 --add-chrname --un-gz Q-Y5F6_1M.se.unal.gz -S Q-Y5F6_1M.se.sam -x /project/BICF/BICF_Core/shared/gudmap/references/GRCh38.p12.v31/hisat2/genome --rna-strandness F -U ./test_data/fastq/small/Q-Y5F6_1M.se_trimmed.fq.gz --summary-file Q-Y5F6_1M.se.alignSummary.txt --new-summary
+  - singularity run 'docker://bicf/gudmaprbkaligner:2.0.0' samtools view -1 -@ 20 -F 4 -F 8 -F 256 -o Q-Y5F6_1M.se.bam Q-Y5F6_1M.se.sam
+  - singularity run 'docker://bicf/gudmaprbkaligner:2.0.0' samtools sort -@ 20 -O BAM -o Q-Y5F6_1M.se.sorted.bam Q-Y5F6_1M.se.bam
+  - singularity run 'docker://bicf/gudmaprbkaligner:2.0.0' samtools index -@ 20 -b Q-Y5F6_1M.se.sorted.bam Q-Y5F6_1M.se.sorted.bam.bai
+  - singularity run 'docker://bicf/gudmaprbkaligner:2.0.0' hisat2 -p 20 --add-chrname --un-gz Q-Y5F6_1M.pe.unal.gz -S Q-Y5F6_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/Q-Y5F6_1M.pe_R1_val_1.fq.gz -2 ./test_data/fastq/small/Q-Y5F6_1M.pe_R2_val_2.fq.gz --summary-file Q-Y5F6_1M.pe.alignSummary.txt --new-summary
+  - singularity run 'docker://bicf/gudmaprbkaligner:2.0.0' samtools view -1 -@ 20 -F 4 -F 8 -F 256 -o Q-Y5F6_1M.pe.bam Q-Y5F6_1M.pe.sam
+  - singularity run 'docker://bicf/gudmaprbkaligner:2.0.0' samtools sort -@ 20 -O BAM -o Q-Y5F6_1M.pe.sorted.bam Q-Y5F6_1M.pe.bam
+  - singularity run 'docker://bicf/gudmaprbkaligner:2.0.0' samtools index -@ 20 -b Q-Y5F6_1M.pe.sorted.bam Q-Y5F6_1M.pe.sorted.bam.bai
   - pytest -m alignData
 
 dedupData:
   stage: unit
   script:
-  - singularity run 'docker://bicf/gudmaprbkdedup:2.0.0' java -jar /picard/build/libs/picard.jar MarkDuplicates I=./test_data/bam/small/Q-Y5JA_1M.se.sorted.bam O=Q-Y5JA_1M.se.deduped.bam M=Q-Y5JA_1M.se.deduped.Metrics.txt REMOVE_DUPLICATES=true
-  - singularity run 'docker://bicf/gudmaprbkdedup:2.0.0' samtools sort -@ 20 -O BAM -o Q-Y5JA_1M.se.sorted.deduped.bam ./test_data/bam/small/Q-Y5JA_1M.se.deduped.bam
-  - singularity run 'docker://bicf/gudmaprbkdedup:2.0.0' samtools index -@ 20 -b ./test_data/bam/small/Q-Y5JA_1M.se.sorted.deduped.bam Q-Y5JA_1M.se.sorted.deduped.bam.bai
+  - singularity run 'docker://bicf/gudmaprbkdedup:2.0.0' java -jar /picard/build/libs/picard.jar MarkDuplicates I=./test_data/bam/small/Q-Y5F6_1M.se.sorted.bam O=Q-Y5F6_1M.se.deduped.bam M=Q-Y5F6_1M.se.deduped.Metrics.txt REMOVE_DUPLICATES=true
+  - singularity run 'docker://bicf/gudmaprbkdedup:2.0.0' samtools sort -@ 20 -O BAM -o Q-Y5F6_1M.se.sorted.deduped.bam ./test_data/bam/small/Q-Y5F6_1M.se.deduped.bam
+  - singularity run 'docker://bicf/gudmaprbkdedup:2.0.0' samtools index -@ 20 -b ./test_data/bam/small/Q-Y5F6_1M.se.sorted.deduped.bam Q-Y5F6_1M.se.sorted.deduped.bam.bai
   - >
     for i in {"chr8","chr4","chrY"}; do 
-      echo "samtools view -b Q-Y5JA_1M.se.sorted.deduped.bam ${i} > Q-Y5JA_1M.se.sorted.deduped.${i}.bam; samtools index -@ 20 -b Q-Y5JA_1M.se.sorted.deduped.${i}.bam Q-Y5JA_1M.se.sorted.deduped.${i}.bam.bai;";
+      echo "samtools view -b Q-Y5F6_1M.se.sorted.deduped.bam ${i} > Q-Y5F6_1M.se.sorted.deduped.${i}.bam; samtools index -@ 20 -b Q-Y5F6_1M.se.sorted.deduped.${i}.bam Q-Y5F6_1M.se.sorted.deduped.${i}.bam.bai;";
       done | singularity run 'docker://bicf/gudmaprbkdedup:2.0.0' parallel -j 20 -k
   - pytest -m dedupData
 
 countData:
   stage: unit
   script:
-  - singularity run 'docker://bicf/subread2:2.0.0' featureCounts -R SAM -p -G /project/BICF/BICF_Core/shared/gudmap/references/GRCh38.p12.v31/genome.fna -T 20 -s 1 -a /project/BICF/BICF_Core/shared/gudmap/references/GRCh38.p12.v31/genome.gtf -o Q-Y5JA_1M.se.featureCounts -g 'gene_name' --primary --ignoreDup -B ./test_data/bam/small/Q-Y5JA_1M.se.sorted.deduped.bam 
-  - singularity run 'docker://bicf/subread2:2.0.0' Rscript ./workflow/scripts/calculateTPM.R --count Q-Y5JA_1M.se.featureCounts
+  - singularity run 'docker://bicf/subread2:2.0.0' featureCounts -T 20 -a /project/BICF/BICF_Core/shared/gudmap/references/GRCh38.p12.v31/genome.gtf -G /project/BICF/BICF_Core/shared/gudmap/references/GRCh38.p12.v31/genome.fna -g 'gene_name' -o Q-Y5F6_1M.se.featureCounts -s 1 -R SAM --primary --ignoreDup ./test_data/bam/small/Q-Y5F6_1M.se.sorted.deduped.bam 
+  - singularity run 'docker://bicf/subread2:2.0.0' Rscript ./workflow/scripts/calculateTPM.R --count ./test_data/counts/small/Q-Y5F6_1M.se.featureCounts
   - pytest -m makeFeatureCounts
 
 makeBigWig:
   stage: unit
   script:
-  - singularity run 'docker://bicf/deeptools3.3:2.0.0' bamCoverage -p 20 -b ./test_data/bam/small/Q-Y5JA_1M.se.sorted.deduped.bam -o Q-Y5JA_1M.se.bw
+  - singularity run 'docker://bicf/deeptools3.3:2.0.0' bamCoverage -p 20 -b ./test_data/bam/small/Q-Y5F6_1M.se.sorted.deduped.bam -o Q-Y5F6_1M.se.bw
   - pytest -m makeBigWig
 
 fastqc:
   stage: unit
   script:
-  - singularity run 'docker://bicf/fastqc:2.0.0' ./test_data/fastq/small/Q-Y5JA_1M.R1.fastq.gz -o .
+  - singularity run 'docker://bicf/fastqc:2.0.0' ./test_data/fastq/small/Q-Y5F6_1M.R1.fastq.gz -o .
   - pytest -m fastqc
 
 dataQC:
   stage: unit
   script:
-  - echo -e  "geneID\tchrom\ttx_start\ttx_end\tTIN" > Q-Y5JA_1M.se.sorted.deduped.tin.xls
+  - echo -e  "geneID\tchrom\ttx_start\ttx_end\tTIN" > Q-Y5F6_1M.se.sorted.deduped.tin.xls
   - for i in {"chr8","chr4","chrY"}; do
-    echo "tin.py -i /project/BICF/BICF_Core/shared/gudmap/test_data/bam/small/Q-Y5JA_1M.se.sorted.deduped.${i}.bam -r /project/BICF/BICF_Core/shared/gudmap/references/GRCh38.p12.v31/bed/genome.bed; cat Q-Y5JA_1M.se.sorted.deduped.${i}.tin.xls | tr -s \"\\w\" \"\\t\" | grep -P \"\\t${i}\\t\";"; done | singularity run 'docker://bicf/rseqc3.0:2.0.0' parallel -j 20 -k >> Q-Y5JA_1M.se.sorted.deduped.tin.xls
+    echo "tin.py -i ./test_data/bam/small/Q-Y5F6_1M.se.sorted.deduped.${i}.bam -r /project/BICF/BICF_Core/shared/gudmap/references/GRCh38.p12.v31/bed/genome.bed; cat Q-Y5F6_1M.se.sorted.deduped.${i}.tin.xls | tr -s \"\\w\" \"\\t\" | grep -P \"\\t${i}\\t\";"; done | singularity run 'docker://bicf/rseqc3.0:2.0.0' parallel -j 20 -k >> Q-Y5F6_1M.se.sorted.deduped.tin.xls
   - pytest -m dataQC
 
 

workflow/tests/test_alignReads.py

@@ -11,13 +11,13 @@ 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-Y5JA_1M.se.unal.gz'))
-	assert os.path.exists(os.path.join(data_output_path, 'Q-Y5JA_1M.se.sorted.bam'))
-	assert os.path.exists(os.path.join(data_output_path, 'Q-Y5JA_1M.se.sorted.bam.bai'))
+	assert os.path.exists(os.path.join(data_output_path, 'Q-Y5F6_1M.se.unal.gz'))
+	assert os.path.exists(os.path.join(data_output_path, 'Q-Y5F6_1M.se.sorted.bam'))
+	assert os.path.exists(os.path.join(data_output_path, 'Q-Y5F6_1M.se.sorted.bam.bai'))
 
 
 @pytest.mark.alignData
 def test_alignData_pe():
-	assert os.path.exists(os.path.join(data_output_path, 'Q-Y5JA_1M.pe.unal.gz'))
-	assert os.path.exists(os.path.join(data_output_path, 'Q-Y5JA_1M.pe.sorted.bam'))
-	assert os.path.exists(os.path.join(data_output_path, 'Q-Y5JA_1M.pe.sorted.bam.bai'))
+	assert os.path.exists(os.path.join(data_output_path, 'Q-Y5F6_1M.pe.unal.gz'))
+	assert os.path.exists(os.path.join(data_output_path, 'Q-Y5F6_1M.pe.sorted.bam'))
+	assert os.path.exists(os.path.join(data_output_path, 'Q-Y5F6_1M.pe.sorted.bam.bai'))

workflow/tests/test_dataQC.py

@@ -10,5 +10,5 @@ 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-Y5JA_1M.se.sorted.deduped.tin.xls'))
+    assert os.path.exists(os.path.join(test_output_path, 'Q-Y5F6_1M.se.sorted.deduped.tin.xls'))
 

workflow/tests/test_dedupReads.py

@@ -11,11 +11,11 @@ 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-Y5JA_1M.se.sorted.deduped.bam'))
-    assert os.path.exists(os.path.join(data_output_path, 'Q-Y5JA_1M.se.sorted.deduped.bam.bai'))
-    assert os.path.exists(os.path.join(data_output_path, 'Q-Y5JA_1M.se.sorted.deduped.chr8.bam'))
-    assert os.path.exists(os.path.join(data_output_path, 'Q-Y5JA_1M.se.sorted.deduped.chr8.bam.bai'))
-    assert os.path.exists(os.path.join(data_output_path, 'Q-Y5JA_1M.se.sorted.deduped.chr4.bam'))
-    assert os.path.exists(os.path.join(data_output_path, 'Q-Y5JA_1M.se.sorted.deduped.chr4.bam.bai'))
-    assert os.path.exists(os.path.join(data_output_path, 'Q-Y5JA_1M.se.sorted.deduped.chrY.bam'))
-    assert os.path.exists(os.path.join(data_output_path, 'Q-Y5JA_1M.se.sorted.deduped.chrY.bam.bai'))
+    assert os.path.exists(os.path.join(data_output_path, 'Q-Y5F6_1M.se.sorted.deduped.bam'))
+    assert os.path.exists(os.path.join(data_output_path, 'Q-Y5F6_1M.se.sorted.deduped.bam.bai'))
+    assert os.path.exists(os.path.join(data_output_path, 'Q-Y5F6_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'))
+    assert os.path.exists(os.path.join(data_output_path, 'Q-Y5F6_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'))
+    assert os.path.exists(os.path.join(data_output_path, 'Q-Y5F6_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'))

workflow/tests/test_fastqc.py

@@ -10,4 +10,4 @@ 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-Y5JA_1M.R1_fastqc.zip'))
\ No newline at end of file
+    assert os.path.exists(os.path.join(test_output_path, 'Q-Y5F6_1M.R1_fastqc.zip'))

workflow/tests/test_getBag.py

@@ -10,4 +10,4 @@ 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, 'Replicate_16-1ZX4.zip'))
\ No newline at end of file
+    assert os.path.exists(os.path.join(test_output_path, 'Replicate_Q-Y5F6.zip'))

workflow/tests/test_getData.py

@@ -10,5 +10,5 @@ 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, 'Study_Q-Y4H0/bagit.txt'))
-    assert os.path.exists(os.path.join(test_output_path, 'Study_Q-Y4H0/data/assets/Study/Q-Y4H0/Experiment/Q-Y4BY/Replicate/Q-Y5F8/hMARIS_SIX2+_RiboDep#1.gene.rpkm.txt'))
\ No newline at end of file
+    assert os.path.exists(os.path.join(test_output_path, 'Replicate_Q-Y5F6/bagit.txt'))
+    assert os.path.exists(os.path.join(test_output_path, 'Replicate_Q-Y5F6/data/assets/Study/Q-Y4GY/Experiment/Q-Y4DP/Replicate/Q-Y5F6/mMARIS_Six2-#3.gene.rpkm.txt'))

workflow/tests/test_inferMetadata.py

@@ -10,5 +10,5 @@ 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-Y5JA_1M.se.inferMetadata.log'))
+    assert os.path.exists(os.path.join(test_output_path, 'Q-Y5F6_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-Y5JA_1M.se.bw'))
+    assert os.path.exists(os.path.join(data_output_path, 'Q-Y5F6_1M.se.bw'))

workflow/tests/test_makeFeatureCounts.py

@@ -11,5 +11,5 @@ 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-Y5JA_1M.se.featureCounts'))
-	assert os.path.exists(os.path.join(data_output_path, 'Q-Y5JA_1M.se.countTable.csv'))
+	assert os.path.exists(os.path.join(data_output_path, 'Q-Y5F6_1M.se.featureCounts'))
+	assert os.path.exists(os.path.join(data_output_path, 'Q-Y5F6_1M.se.countTable.csv'))

workflow/tests/test_trimData.py

@@ -10,10 +10,10 @@ 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-Y5JA_1M.se_trimmed.fq.gz'))
+    assert os.path.exists(os.path.join(test_output_path, 'Q-Y5F6_1M.se_trimmed.fq.gz'))
 
 
 @pytest.mark.trimData
 def test_trimData_pe():
-    assert os.path.exists(os.path.join(test_output_path, 'Q-Y5JA_1M.pe_R1_val_1.fq.gz'))
-    assert os.path.exists(os.path.join(test_output_path, 'Q-Y5JA_1M.pe_R2_val_2.fq.gz'))
\ No newline at end of file
+    assert os.path.exists(os.path.join(test_output_path, 'Q-Y5F6_1M.pe_R1_val_1.fq.gz'))
+    assert os.path.exists(os.path.join(test_output_path, 'Q-Y5F6_1M.pe_R2_val_2.fq.gz'))