Questions about usage and output

[Faewks]

Hi, first of all: Thank you for this tool!

I have some question related the output and the usage of ToulligQC. I'm running version 2.2

• at the end of the Readme.md you mentioned that the output should look like this: RUN_ID ├── report.html ├── report.data └── images └── plots.html └── plot.png

  For me it looks like this after this program call:

toulligqc --report-name <ReportName> \ --telemetry-source /Path/To/sequencing_telemetry.js \ --sequencing-summary-source /PAth/To/sequencing_summary.txt \ --output-directory /Path/To/OutputDirectory/

RUN_ID ├── report.html ├── report.data └── images └── plots.html

Do I miss a option or do I missunderstand your outputgraph?

• The second thing I have to ask, is if the Kit "SQK-PCB109" is not (yet) included into ToulligQC? I have tried it with following command:

toulligqc --report-name <ReportName> \ --telemetry-source /Path/To/sequencing_telemetry.js \ --sequencing-summary-source /Path/To/sequencing_summary.txt \ --sequencing-summary-source /Path/To/barcoding_summary_pass.txt \ --sequencing-summary-source /Path/To/barcoding_summary_fail.txt \ --barcodes BP01,BP02,BP03,BP04,BP05,BP06,BP07,BP08,BP09,BP10,BP11,BP12 \ --output-directory /Path/To/OutputDirectory/

and got ERROR: No known barcode found in provided list of barcodes

Thank you in advance.

[jourdren]

Dear Faewks,

Thanks for reporting this issue. I've just made a commit to fix this issue https://github.com/GenomiqueENS/toulligQC/commit/e7c3a86cf458315a6e2e3e9d7dfb9a5b40f7d872.

However, you can bypass this issue if in the barcode_arrangement column of your sequencing_summary.txt file, the barcodes are named like barcodeXX. In this case, just rename in your command line BPXX by barcodeXX, and ToulligQC will work!

Tell me, if this workaround works for you.

Best regards,

Laurent.

[Faewks]

Dear Laurent, thank you for your quick replay and fix.

Your suggested workarounds works flawlessly for the barcode issue.

May I still point you to the first point where I thought, that the .png files should also be created automatically? Should this be the case, or should I just do it by hand with the .html files?

Best regards, Faewks.

[jourdren]

Dear Faewks,

Great news to hear.

Unfortunately, ToulligQC cannot save PNG images as the plots are interactive and made with Plotly that use HTML/Javascript behind. You must use screenshot feature of your OS/web browser (Firefox's one is great) to save plots as PNG images.

Best regards,

Laurent.

PS: I will soon close this issue.

[Faewks]

Ok, Thank you for the tipps and I will close this issue.

Best regards, Faewks.