Implementation of the sample sheet in the pipeline

[marissaDubbelaar]

It could be suggested that we create the following annotation for the input file:

• sample ID,
• vcf file
• alleles (A*01:01),
• peptide sequences file*,
• protein file

• The question here is where fo the id and sequence stand for (UniProt id and peptide sequence). Would it not be interesting to include the associated protein here as well?

[christopher-mohr]

alleles is mandatory, ONE of vcf file, peptide sequences file and protein file is mandatory

[marissaDubbelaar]

References to alter the files:

https://github.com/marissaDubbelaar/mhcquant/blob/master/bin/check_samplesheet.py
https://github.com/marissaDubbelaar/mhcquant/blob/master/modules/local/samplesheet_check.nf

[jonasscheid]

Proposed solution for the sample sheet structure:

SampleID | Alleles | FileName

where Alleles column contains EITHER a string of alleles (A*02:01;A*24:01;B*07:02;B*08:01;C*04:01;C*07:01) OR a text file containing one allele per line (no header)

and FileName contains EITHER a tsv file containing the peptides like
id | sequence
peptid1 | SYFPEITHI

OR a fasta file containing protein sequences
OR an annotated vcf file

The input of those provided files need to be validated

[marissaDubbelaar]

Maybe we can rename SampleID to ID to keep the uniform annotation

[christopher-mohr]

As discussed we will stick to the columns sample, alleles and filename.

[marissaDubbelaar]

@jonasscheid, @christopher-mohr
I noticed that the check_requested_models.py doesn't take "A01:01;A02:01" as input but "HLA-A01:01;HLA-A02:01".
So we need to update this in the check_samplesheet.py that it checks whether the HLA types start with "H-2-", or "HLA-" or we need to remove this check from the check_requested_models.py

[jonasscheid]

How about leaving the mouse nomenclature as is and allow 2 notations for the HLA alleles: With and without "HLA-" prefix.
I noticed that I need to allow mouse alleles in the check_samplesheet.py as well so I need to update it anyway. Lets wait on @christopher-mohr 's suggestion

[ggabernet]

Done in #124