Closed Faewks closed 2 years ago
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.
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.
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.
Ok, Thank you for the tipps and I will close this issue.
Best regards, 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.pngFor 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?
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.