Paramter passing to BIGBIO_QUANTMS:QUANTMS:DIA:INDIVIDUAL_ANALYSIS

[enryH]

I put the issue here, although I still run with quantms...

I wonder if the parameters to BIGBIO_QUANTMS:QUANTMS:DIA:INDIVIDUAL_ANALYSIS can be passed on using a meta map, avoiding to parse the the parameters from the log file.

diann   --lib empirical_library.parquet \
        --f 13_1_2_S2-A7_1_540.d \
        --fasta Kluyveromyces_lactis_UP000000598_2025_11_23.fasta \
        --threads 12 \
        --verbose 3 \
        --temp ./ \
        --mass-acc $(cat assemble_empirical_library.log | grep "Averaged recommended settings" | cut -d ' ' -f 11 | tr -cd "[0-9]") \
        --mass-acc-ms1 $(cat assemble_empirical_library.log | grep "Averaged recommended settings" | cut -d ' ' -f 15 | tr -cd "[0-9]") \
        --window $(cat assemble_empirical_library.log | grep "Averaged recommended settings" | cut -d ' ' -f 19 | tr -cd "[0-9]") \
        --no-ifs-removal \
        --no-main-report \
        --relaxed-prot-inf \
        --pg-level 2 \
        ${mod_flags} \

Looks to me as if these parameters can be specified to match the recommendations:

https://github.com/vdemichev/DiaNN?tab=readme-ov-file#changing-default-settings

[ypriverol]

Should we move this to the step where they are produced; rather than this step and if the values are not found then we use default? @yueqixuan @daichengxin.

When we do the preliminary analysis by file in the log files DIANN writes the final best calibrated values for these two variables; but I agree with you we could capture that in the output of the previous step that does that; in a meta variable.

[yueqixuan]

@ypriverol Great idea! I'll give it a try and work on implementing this.