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genepi / umi-pipeline-nf

Nextflow pipeline to analyze ONT UMI Sequencing data
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Interpreting test output #65

Closed ebwinter95 closed 4 months ago

ebwinter95 commented 4 months ago

Hi, I am looking for some clarification in interpreting the output of the test data. I am seeing these directories within the output directory: barcode02/, barcode03/, freebayes/, and nextflow_stats/. But between barcode02/ vs. barcode03/, there are differences. Any information about why the barcode outputs are different would be greatly appreaciated.

test output directory:

barcode02/align/raw barcode02/clustering/raw barcode02/fastq_filtered/raw barcode02/fastq_umi/raw barcode02/stats/raw

barcode03/align/ barcode03/clustering/ barcode03/fastq/ barcode03/fastq_filtered/raw barcode03/fastq_umi/ barcode03/stats/

AmstlerStephan commented 4 months ago

Hi, Barcode02 does not have any clusters above the minimal number of reads per cluster threshold. Therefore there are no consensus reads created. Barcode03 contains 84 clusters above the threshold, for which the consensus is created and further processed.

I am currently working on implementing nf-test for the whole pipeline, which also includes different, clearer test cases.

I hope this helps to interpret the results.

ebwinter95 commented 4 months ago

Thank you! That helps a lot