Update typingQC to align with mikrokondo and CDC #21
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Updating the template for TypingQC pipeline
Initial Release of TypingQC v1.0.0
Update to Version 1.0.1
1.0.2 Release
…_count quality metric
…puts for formatting improvement
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emarinier
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Thanks Kyla. I left a few comments, but it looks good to me.
| #QC_MESSAGES Updates | ||
| #Matches the non-actionable cgMLST loci found INFO message and strips it from qc_messages | ||
| CGMLST_LOCI_INFO_PATTERN = re.compile(r"INFO: Number of cgMLST\d+ loci found \(n=\d+\)") | ||
| def filter_qc_messages(qc_messages): |
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If I'm understanding this correctly that this is parsing SISTR output (and not output we easily have control over), then this seem reasonable to me.
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Yes exactly - it causes a lot of extra text in IRIDA Next metadata fields and serves no use for those in the lab who are analyzing the data!
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| if 'FAIL' in typingqc_upper: | ||
| return 'pending' | ||
| return 'pending', quality_metrics |
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I think two returned items is okay for now, but if gets more complicated, then it might be worth making a simple object to encapsulate all of it and return that object back.
| SAMPLE5,SALM003,https://raw.githubusercontent.com/phac-nml/typingQC/dev/tests/data/SALM003.flat_sample.json.gz,Salmonella enterica,FAILED,Kentucky | ||
| SAMPLE6,LIST001,https://raw.githubusercontent.com/phac-nml/typingQC/dev/tests/data/LIST001.flat_sample.json.gz,Listeria monocytogenes,PASSED, | ||
| SAMPLE7,LIST001,https://raw.githubusercontent.com/phac-nml/typingQC/dev/tests/data/LIST001.flat_sample.json.gz,Listeria monocytogenes,PASSED, | ||
| SAMPLE1,EC001,https://raw.githubusercontent.com/phac-nml/typingQC/update/tests/data/EC001.flat_sample.json.gz,Escherichia coli,PASSED,O157:H7 |
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Reminder to update these paths later.
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Summary
Updates to three typingQC pipeline modules to support a new mikrokondo QA field, fix a pre-existing schema mismatch, and add serovar nomenclature handling.
sequenceQC.py
wgmlst_loci_countto QA handling: captured as a warning test but returnsPNC_FAIL_MESSAGEon failureCHECKM_TESTconstant:checkm_contamination→checkm2_contaminationto match current mikrokondo JSON schemasistrQC.py
INFO: Number of cgMLST loci foundmessage fromqc_messagesbefore reportingquality_metricsreports a warning instead of a raw FAIL messagevalidateSerotype.py
Panama→Panama/Houston,Sendai→Miamiquality_metricsPR checklist
nf-core lint).nextflow run . -profile test,docker --outdir <OUTDIR>).CHANGELOG.mdis updated.README.mdis updated (including new tool citations and authors/contributors).