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Fix small bug when extracting read type from bowtie2 #154

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merged 3 commits into from
Jan 23, 2025
Merged

Fix small bug when extracting read type from bowtie2 #154

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fee626d
In cases where the READID has 'YT' in it, this code will fail since i…
harmonbhasin Jan 22, 2025
127eefd
Update CHANGELOG.md
harmonbhasin Jan 22, 2025
9ac810c
Merge branch 'dev' into harmon_bug_fix
willbradshaw Jan 22, 2025
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Original file line number Diff line number Diff line change
Expand Up @@ -9,6 +9,7 @@
- Added Fastp adapter trimming after running BBDuk in the EXTRACT_VIRAL_READS subworkflow.
- Implement masking of viral genome reference in index workflow with MASK_GENOME_FASTA to remove adapter, low-entropy and repeat sequences.
- Remove TRIMMOMATIC and BBMAP from the pipeline.
- Fixed bug in extractUnconcReadID that would cause the pipeline to fail if it contained the string 'YT' in the read id.

# v2.6.0.0
- Updated version to reflect the new versioning scheme, which is described in `docs/version_schema.md`.
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2 changes: 1 addition & 1 deletion modules/local/extractUnconcReadIDs/main.nf
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Expand Up @@ -22,7 +22,7 @@ process EXTRACT_UNCONC_READ_IDS {
continue
id = line_split[0]
try:
status_field = [f for f in line_split if "YT" in f][0]
status_field = [f for f in line_split if "YT:Z:" in f][0]
status = re.findall("YT:Z:(.*)", status_field)[0]
except:
print(line_split)
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