This PR completes the parameterisation of all the currently created and used R scripts.
Here is a list of the scripts changed in this PR with a short description of the files functionality:
[ ] bin/concat_chroms.R: R script that can be run from the command line. Concatenates SAIGE output files that have been generated by running SAIGE in separate chromosomal regions and creates the unified final csv file that contains all the examined sites in the GWAS performed
[ ] bin/DTable.R: Script with a utility function, to use the DT R package and render an interactive table in the rmarkdown report.
[ ] bin/subset_gwascat.R:
[ ] bin/gwas_report.Rmd: The rmarkdown file that will generate the GWAS html report. Here updated to display the SAIGE output as an interactive DT data table, in addition to the previously added GWAS catalogue.
Also updated:
[ ] main.nf, to include docs and code changes in scripts and add parameterised scripts
[ ] nextflow.config, to include new exposed parameters from the parameterised R scripts
This PR completes the parameterisation of all the currently created and used R scripts.
Here is a list of the scripts changed in this PR with a short description of the files functionality:
bin/concat_chroms.R: R script that can be run from the command line. Concatenates SAIGE output files that have been generated by running SAIGE in separate chromosomal regions and creates the unified final csv file that contains all the examined sites in the GWAS performedbin/DTable.R: Script with a utility function, to use theDTR package and render an interactive table in the rmarkdown report.bin/subset_gwascat.R:bin/gwas_report.Rmd: The rmarkdown file that will generate the GWAS html report. Here updated to display the SAIGE output as an interactive DT data table, in addition to the previously added GWAS catalogue.Also updated:
main.nf, to include docs and code changes in scripts and add parameterised scriptsnextflow.config, to include new exposed parameters from the parameterised R scriptsHere's an example CloudOS link with the report (check temporarily named
MultiQCslot): https://cloudos.lifebit.ai/public/jobs/5f57a8b617041401122ad179