BCL delivery process

[chaetognatha]

The samplesheet for rawdata deliveries will be called the same as every other, but it will only contain project ID on one line, no commas or anything else, so a file with one line that is the project ID! (there should also be flags to specify both project ID and rawdata delivery, in which case we shouldnt need a samplesheet at all!)

[chaetognatha]

Perhaps it will be useful to have this line that I use to do md5sum over multiple processes on LSENS:

module load parallel/20220722
raw=$1
parallel -j8 "md5sum {} >> ${raw}/md5.txt" ::: $(find ${raw}/Data -type f -print)
#forgot that I also need to do this
sed -i s'/\/projects\/.*\/upload\/\w\+/./g' ${raw}/md5.txt

[lokeshbio]

We should probably include what kind of delivery each project requires in the sample_sheet! At the moment, the example samplesheet look like this:

[Yggdrasil_Projects],,,
Project_ID,bcl,fastq,fastq_screen,fastq_screen_ref
2022_000,0,1,0,NA

If we keep adding more pipelines, it is not sustainable to keep adding columns! i would rather have these end deliveries set as Keys like BCL, FASTQ, FASTQ_SCREEN, RNASEQ, METHYLSEQ and so on.. that they are just in one column! then we can have these as binary parameters in Yggdrasil!

#In samplesheet

[Yggdrasil_Projects],,,
Project_ID,Delivery
2022_000,FASTQ
2022_001,RNASEQ

# Then in Yggdrasil nextflow script: we can set these parameters as

params.rnaseq = TRUE #specifically for 2022_001

[lokeshbio]

BCL delivery process needs to be discussed

[lokeshbio]

Hi @chaetognatha , Here is the example of the samplesheet above for a run that could potentially contain different deliveries in the same run. In this above example it is one project with RNASEQ and the other with FASTQ. If we have a test run and a test samplesheet like this, then I can test to run Yggdrasil all the way from raw-data to getting the rnaseq output!