Used betterd CHRs for tests.

.gitlab-ci.yml

@@ -69,7 +69,7 @@ dedupData:
   - 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 -@ `nproc` -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 -@ `nproc` -b ./test_data/bam/small/Q-Y5JA_1M.se.sorted.deduped.bam Q-Y5JA_1M.se.sorted.deduped.bam.bai
-  - for i in {"chrNC_000001.11","chrNC_000002.12","chrNC_000019.10"}; do 
+  - 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 -@ `nproc` -b Q-Y5JA_1M.se.sorted.deduped.${i}.bam Q-Y5JA_1M.se.sorted.deduped.${i}.bam.bai;";
       done | singularity run 'docker://bicf/gudmaprbkdedup:2.0.0' parallel -j `nproc` -k
   - pytest -m dedupData
@@ -89,7 +89,7 @@ fastqc:
 inferMetadata:
   stage: unit
   script:
-  - for i in {"chrNC_000001.11","chrNC_000002.12","chrNC_000019.10"}; do
+  - 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 `nproc` -k > Q-Y5JA_1M.se.sorted.deduped.tin.xls
   - pytest -m inferMetadata
 

workflow/tests/test_dedupReads.py

@@ -13,9 +13,9 @@ data_output_path = os.path.dirname(os.path.abspath(__file__)) + \
 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.chrNC_000001.11.bam'))
-    assert os.path.exists(os.path.join(data_output_path, 'Q-Y5JA_1M.se.sorted.deduped.chrNC_000001.11.bam.bai'))
-    assert os.path.exists(os.path.join(data_output_path, 'Q-Y5JA_1M.se.sorted.deduped.chrNC_000002.12.bam'))
-    assert os.path.exists(os.path.join(data_output_path, 'Q-Y5JA_1M.se.sorted.deduped.chrNC_000002.12.bam.bai'))
-    assert os.path.exists(os.path.join(data_output_path, 'Q-Y5JA_1M.se.sorted.deduped.chrNC_000019.10.bam'))
-    assert os.path.exists(os.path.join(data_output_path, 'Q-Y5JA_1M.se.sorted.deduped.chrNC_000019.10.bam.bai'))
\ No newline at end of file
+    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'))