Bowtie1: Handle missing word in log output.

Closes #1615
MultiQC · Jan 25, 2022 · 18c9faa · 18c9faa
1 parent d49f0e2
commit 18c9faa
Show file tree

Hide file tree

Showing 2 changed files with 4 additions and 2 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -30,6 +30,8 @@
 
 - **bclconvert**
   - Handle change in output format in v3.9.3 with new `Quality_Metrics.csv` file ([#1563](https://github.com/ewels/MultiQC/issues/1563))
+- **bowtie**
+  - Minor update to handle new log wording in bowtie v1.3.0 ([#1615](https://github.com/ewels/MultiQC/issues/1615))
 - **CCS**
   - Tolerate compound IDs generated by pbcromwell ccs in the general statistics ([#1486](https://github.com/ewels/MultiQC/pull/1486))
   - Fix report parsing. Update test on attributes ids ([#1583](https://github.com/ewels/MultiQC/issues/1583))

diff --git a/multiqc/modules/bowtie1/bowtie1.py b/multiqc/modules/bowtie1/bowtie1.py
@@ -58,8 +58,8 @@ def parse_bowtie_logs(self, f):
         parsed_data = {}
         regexes = {
             "reads_processed": r"# reads processed:\s+(\d+)",
-            "reads_aligned": r"# reads with at least one reported alignment:\s+(\d+)",
-            "reads_aligned_percentage": r"# reads with at least one reported alignment:\s+\d+\s+\(([\d\.]+)%\)",
+            "reads_aligned": r"# reads with at least one(?: reported)? alignment:\s+(\d+)",
+            "reads_aligned_percentage": r"# reads with at least one(?: reported)? alignment:\s+\d+\s+\(([\d\.]+)%\)",
             "not_aligned": r"# reads that failed to align:\s+(\d+)",
             "not_aligned_percentage": r"# reads that failed to align:\s+\d+\s+\(([\d\.]+)%\)",
             "multimapped": r"# reads with alignments suppressed due to -m:\s+(\d+)",