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vari-bbc / demultiplex

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FastQC/multiQC not needed for Undetermined files #8

Closed VAIgenomics closed 3 years ago

VAIgenomics commented 3 years ago

There is minimal benefit to getting this data for Undetermined files, while removing it would greatly speed up the dmux process. I believe we just no longer need symlinks into each project directory (rundirectory/Data/Intensities/Basecalls/projectdirectory).

genomics-kl commented 3 years ago

We will work on this asap.

VAIgenomics commented 3 years ago

thanks.

joowkim commented 3 years ago

Hello all,

I updated the demultiplex pipeline to skip FastQC/multiQC for the undetermined files and tried it out with a couple of test runs. I think it works okay. You can use it with the below command.

git clone https://github.com/vari-bbc/demultiplex.git qsub -q genomics demultiplex/bcl2fastq_snake.sh

genomics-kl commented 3 years ago

Closed by b09be60ba