Modify PROTEOMICS subworkflow logic to pool fractions and technical replicates for a single biological replicate

[JTL-lab]

Note:

• Will need to add column for 'fraction' to samplesheet, which can be NaN for RNA samples but will be required for protein samples.
• Example samplesheet scenario:

biological_rep,frac,technical_rep
1,1,1
1,1,2
1,2,1
1,2,2
1,3,1
1,3,2

[JTL-lab]

New samplesheet formatting plan:

sample_name,sample_path,condition,sample_type
A,A.01.isoseq.flnc.bam,control,RNA
B,B.01.isoseq.flnc.bam,control,RNA
C,C.01.isoseq.flnc.bam,disease,RNA
D,D.01.isoseq.flnc.bam,disease,RNA
A,A_injection1.raw,control,protein
A,A_injection2.raw,control,protein
A,A_injection3.raw,control,protein
C,C_injection1.raw,control,protein
C,C_injection2.raw,disease,protein
C,C_injection3.raw,disease,protein

Rules for samplesheet:

• RNA and protein samples that should go together should have matching sample_name and condition values.
• Biological replicates should have unique sample names.
• Technical replicates are assumed to have the same sample name.