When submitting the sample sheet check needs to have arguments submitted along side, the argument is the "SampleSheet_Name.csv"
The Rmd both have parameters that need to be added in the shell script look at which paramters need to be added in the YAML sectio nat the top of the Rmd document
to submitt the Rmd run this code in the shell
Rscript -e 'library(rmarkdown);rmarkdown::render("Name_of_Rmd.Rmd", params = list(Name = "Bipolar Study", SampleSheet = "SampleSheet_NCBI.csv", Mset = "NCBI_Mset.rdat", RGset = "NCBI_RGset.rdat"), output_file = "/mnt/data1/Array_Projects/Dummy_Data/test.html")'
Technical QC has 5 parameters
Name: Study_Name
SampleSheet: SampleSheet_Name.csv
PathTOProjectFolder: /mnt/data1/Array_Projects/...
Mset: Mset_Name.rdat
RGset: RGset_Name.rdat
Full QC has 10 Name: Name_Of_Study
SampleSheet: SampleSheet.csv
PathTOProjectFolder: /mnt/data1/Array_Projects/...
Mset: Mset_Name.rdat
RGset: RGset_Name.rdat
IntensityThreshold: 1000
Genotype: GenotypeTable.csv
SamplesPassed: SamplesPassedQC.csv
SamplesFailed: SamplesFailedQC.csv
Normalised: Samples_Normalised.rdat
intensity threshold has a default of a 1000 so if it is not specified in params it will be set to that You have to rename all the output files as the names you would like them to be saved as.