Runs the Illumina TSO500 local analysis app. Note: this version of the app has been designed to support the analysis pipeline being run multiple times for a single run, i.e. for a 48 sample run, the samplesheet is split into 3 separate samplesheets containing up to 16 samples each. That process is handled by the automated scripts, and the pipeline set off once for each samplesheet. It therefore renames certain files and outputs to reflect this, e.g. the MetricsOutput.tsv file is renamed to MetricsOutputPart1.tsv.
- TSO500_ruo - a zip file (originally provided by Illumina) containing the TSO500 local analysis app.
- DNAnexus project name- provided as a string. NB input is not the project ID
- runfolder name (string)
- Samplesheet
- analysis_options - a string which can be passed to the ruo command line
- The following command was used to download the files: dx download -r project_name:runfolder_name
- Note: The runfolder is no longer expected to be archived (e.g .tar)
- Once the files are downloaded to a folder, the path is provided to TruSight_Oncology_500_RUO.sh
- Runs the TruSight_Oncology_500_RUO.sh (within the TSO500 local app zip file) providing arguments for analysis folder, runfolder, samplesheet, resourcesFolder and any other analysis options given as an input ($analysis_options)
- output files are organised to allow them to be accessed by downstream analyses such as coverage
- RUO_stdout.txt - STDout from RUO. Saved into /logs
- The analysis folder. Saved into /analysis_folder
- zipped results folder for each sample
- fastqs - the content of analysis_folder/Logs_Intermediates/CollapsedReads (contains fastqs and all logs)
- stitchedrealigned BAMs - the content of analysis_folder/Logs_Intermediates/StitchedRealigned (contains BAMs and all logs)
- results vcfs - the content of analysis_folder/Results (contains all results vcfs)
- metrics_tsv file - An copy of the MetricsOutput.tsv is output into /QC so it can be accessed by multiqc.
- QC files - MultiQC compatible files saved to /QC (currently bclconvert stats files- the location of these is updated in the current version)
- Only tested from starting point of BCLs
- analysis_options is not thoroughly tested.