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nf-core / proteomicslfq

Proteomics label-free quantification (LFQ) analysis pipeline
https://nf-co.re/proteomicslfq
MIT License
33 stars 19 forks source link

When the identification part is only relevant - proteomicslfq fail #68

Closed ypriverol closed 4 years ago

ypriverol commented 4 years ago

@julianus @timosachsenberg :

When running the id part only, I guess the proteomicslfq node should only report the protein inference and not the quant part. Currently, I have an error like for this dataset: https://github.com/bigbio/proteomics-metadata-standard/blob/master/annotated-projects/PXD018241/sdrf-phosphoproteomics.tsv

g File '/homes/pst_prd/.OpenMS/OpenMS.ini' is deprecated. Updating missing/wrong entries in '/homes/pst_prd/.OpenMS/OpenMS.ini' with defaults! Unknown (or deprecated) Parameter 'xtandem_executable' given in outdated parameter file! Ignoring parameter. Unknown (or deprecated) Parameter 'omssa_executable' given in outdated parameter file! Ignoring parameter. Default-Parameter 'temp_dir' overridden: '' --> '/nfs/pride/work/archive/oms-platform/temp/'! Unknown (or deprecated) Parameter 'swissprot' given in outdated parameter file! Ignoring parameter. Default-Parameter 'threads' overridden: '1' --> '2'! Error: Unexpected internal error ((Fraction Group, Fraction, Label) combination can only appear once)

timosachsenberg commented 4 years ago

hmm this sounds more like a problem with experimental design. let me check

timosachsenberg commented 4 years ago

maybe this typo?

comment[technical replcate]

ypriverol commented 4 years ago

Going for it