Merge pull request #428 from jodyphelan/dev

bump version
jodyphelan · Feb 24, 2025 · 9757c14 · 9757c14
2 parents bd94ce5 + ca1ff20
commit 9757c14
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Showing 2 changed files with 6 additions and 3 deletions.
diff --git a/tbprofiler/__init__.py b/tbprofiler/__init__.py
@@ -9,4 +9,4 @@
 from .plugins import *
 from .rules import *
 
-__version__ = "6.6.0"
+__version__ = "6.6.3"
diff --git a/tests/run_test.py b/tests/run_test.py
@@ -71,8 +71,11 @@ def test_collate():
 
 def test_tbp_parser():
     run_cmd("git clone https://github.com/theiagen/tbp-parser.git")
-    run_cmd("samtools index bam/por5A_fastq.bam")
-    run_cmd('python tbp-parser/tbp_parser/tbp_parser.py results/por5A_freebayes.results.json bam/por5A_fastq.bam    -o "example-tbp-parser"    --min_depth 12     --min_frequency 0.9     --sequencing_method "Illumina NextSeq"    --operator "John Doe"')
+    os.mkdir("tbp-parser/tb-profiler-test")
+    os.chdir("tbp-parser/tb-profiler-test")
+
+    run_cmd("samtools index ../../bam/por5A_fastq.bam")
+    run_cmd('python ../tbp_parser/tbp_parser.py ../../results/por5A_freebayes.results.json ../../bam/por5A_fastq.bam    -o "example-tbp-parser"    --min_depth 12     --min_frequency 0.9     --sequencing_method "Illumina NextSeq"    --operator "John Doe"')
     test_text = ','.join([l.strip().split(',')[:-2] for l in open("example-tbp-parser.looker_report.csv")][1])
     target_text = "por5A_freebayes,Illumina NextSeq,U,S-Interim,U,U,R,R,R,U,S,U,S,R,R,U,lineage4,DNA of Mycobacterium tuberculosis species detected"
     assert test_text == target_text