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Here is a review on the last training I did on ann nnU-Net for spinal canal segmentation.
I went back on the data I used for the previous training and the data used for [the kaggle competition](https…
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We'd like to be able to determine at a glance if any samples failed QC checkpoints in the pipeline.
Produce a summary file that reports Pass/Fail status for each sample, for each QC checkpoint. The…
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https://github.com/sgsutcliffe/Wastewater_Analysis_Pipeline/blob/6e0437f43278bb270f0eec276783bbfaf3755aa1/QC_parallelization_V2.py#L34
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## New feature
It would be nice to have a special error class or function for pipeline-level errors or warnings, that help distinguish pipeline-defined (conditional) errors versus Nextflow level er…
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The following command line has been used to run the pipeline:
`nextflow run main.nf -profile az_test -w az://orange -ansi-log false -resume -with-dag dag.png`
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This error message occurs afte…
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I need to register C spine T2w images (either `0.28 x 0.28 x 1.3 mm` or `0.8 iso mm`) of subjects with cord compression to the PAM50 template. I have SC seg and disc labels (1 to 10) available.
> […
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Hello,
The header of the .obo file of the Rolling ontology build (and maybe other files, I didn't check all) should include not just the date, but also a timestamp, since it's built multiple times…
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Hi! I have this error that not recognize the files in .fastq
Execution cancelled -- Finishing pending tasks before exit
-[nf-core/rtnanopipeline] Pipeline completed with errors-
WARN: There's no…
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Hi, I'm trying to run multiqc on my homemade pipeline. Every useful log for qc goes into the `qc` directory (inside `$PWD`).
I even managed to add a different search folder for a tool I messed up its…
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### Description of feature
Calculate the percentage of PacBio read data filtered before alignment. This was flagged by Kamil.