8000 Peptides are sometimes removed in the output when an unmodified sequence in present in the input · Issue #258 · nf-core/epitopeprediction · GitHub
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Peptides are sometimes removed in the output when an unmodified sequence in present in the input #258

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steffenlem opened this issue Jan 23, 2025 · 1 comment
Open

Peptides are sometimes removed in the output when an unmodified sequence in present in the input #258

steffenlem opened this issue Jan 23, 2025 · 1 comment
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@steffenlem
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Description of the bug

Hi,

the pipeline seems to sometimes remove rows/peptides with modifications / the same 'sequence' but different 'peptidoform'.
e.g.:
input:

KAM(Oxidation)GYFLKH
KAMGYFLKH

yielding only KAMGYFLKH in the output.

But this is not consistent for all peptides. In my tests around equal peptides with modifications were kept and equal were removed.

e.g.

ATGDMSGLLK
ATGDM(Oxidation)SGLLK

Can both be found in the output.

Best,
Steffen

Command used and terminal output

nextflow run nf-core/epitopeprediction -r 2.2.1 \
    --input input_sheet.csv \
    --outdir ./results \
    --min_peptide_length 8 \
    --max_peptide_length 15 \
    --min_peptide_length_class2 8 \
    --max_peptide_length_class2 30 \
    --tools netmhcpan-4.1,netmhciipan-4.1 \
    --netmhcpan_path netMHCpan-4.1b.Linux.tar.gz \
    --netmhciipan_path netMHCIIpan-4.1a.Linux.tar.gz \
    -profile cfc

Relevant files

input_sheet.csv

System information

No response
@steffenlem steffenlem added the bug Something isn't working label Jan 23, 2025
@jonasscheid
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@steffenlem Can you check again if this happens with the new release 3.0.0?

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@steffenlem @jonasscheid
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