nyu-molecular-pathology / demux-nf Goto Github PK

Right now only 'output/Unaligned/passed0' is used for deploying a new NGS580 based on demultiplexing results, but there could be multiple 'passed' directories, need to update deploy-NGS580 method to use variable number of fastq dirs

The yellow color currently used for 'C' grade undetermined read counts in the NextSeq report is too light and hard to read, need to adjust it for better visibility.

Need to convert the Demultiplex_Stats.htm table output by bcl2fastq to one or more .csv formatted tables for easier usage and importing elsewhere.

Need to develop Docker and/or Singularity containers for bcl2fastq to enable usage of pipeline on systems that support them.

The subdirectory in the output dir which holds the demultiplexed .fastq.gz files has a dynamically generated name based on the contents of the sample sheet used for demultiplexing. This creates inconsistency when trying to figure out the path to the fastq files for downstream usages. Need to come up with a script or method that will create a relative symlink to the output directory. Need to consider how output directories are created based on the samplesheet project name, and sample project names.

The current demultiplexing report shows the total PF clusters ('PF Clusters' column in Demultiplexing htm file). However, this does not reflect the true number of PF clusters that passed quality thresholds ('% PF Clusters'). The report needs to be updated to show the percent of PF clusters that passed, in order to reflect quality control criteria.

references:

https://support.illumina.com/content/dam/illumina-support/documents/documentation/software_documentation/bcl2fastq/bcl2fastq_letterbooklet_15038058brpmi.pdf (page 24-35)

Need to get PDF output for custom demultiplexing report, currently giving errors about missing LaTeX .sty files

Need to develop methods for the pipeline to make outbound API calls during processing in order to update future LIMS/LIS systems of demultiplexing status.

Need to add the steps from this repo to the pipeline;
https://github.com/stevekm/fastq-checker