Fix test and pin bowtie2=2.5.2, addressing issue #21

bede · Oct 23, 2023 · 3568169 · 3568169
1 parent 902e220
commit 3568169
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diff --git a/environment.yml b/environment.yml
@@ -8,6 +8,6 @@ dependencies:
   - pip
   - samtools>=1.17
   - minimap2>=2.26
-  - bowtie2=2.4.5
+  - bowtie2=2.5.2
   - gawk>=5.1.0
   - bedtools>=2.31.0
diff --git a/tests/test_all.py b/tests/test_all.py
@@ -240,7 +240,7 @@ def test_rename():
     first_line = get_first_line_of_gzip_file(
         out_dir / "tuberculosis_1_2.clean_1.fastq.gz"
     )
-    assert first_line == "@1 /1"
+    assert first_line == "@1/1"
     shutil.rmtree(out_dir, ignore_errors=True)