Some users importing DIA-NN results into Skyline have run into issues with the filenames of the speclib and report not matching in the way BlibBuild expects them to. So far users have been giving the path to the speclib file and BlibBuild expects to be able to automatically find the TSV report in the same directory by looking for a TSV file having the correct columns and sharing some of its basename with the speclib file. This has turned out to be pretty brittle since users are free to name the speclib and TSV outputs very differently and save them to separate subdirectories. So we need to change the way users specify what DIA-NN file to import.

I've sent an email to Vadim about updating DIA-NN to produce a manifest file we can tell users to point at instead to solve this problem. If he's not willing to do a manifest file, it looks like parsing the command-line from the .log file will be the next best thing:

diann.exe --f C:\DIA-NN\1.8\2021MK017_EVBO_FCB\2021MK017_EVBO_001_01_2ug.raw --f C:\DIA-NN\1.8\2021MK017_EVBO_FCB\2021MK017_EVBO_002_01_2ug.raw --f C:\DIA-NN\1.8\2021MK017_EVBO_FCB\2021MK017_EVBO_003_01_2ug.raw --f C:\DIA-NN\1.8\2021MK017_EVBO_FCB\2021MK017_EVBO_004_01_2ug.raw --f C:\DIA-NN\1.8\2021MK017_EVBO_FCB\2021MK017_EVBO_005_01_2ug.raw --f C:\DIA-NN\1.8\2021MK017_EVBO_FCB\2021MK017_EVBO_006_01_2ug.raw --f C:\DIA-NN\1.8\2021MK017_EVBO_FCB\2021MK017_EVBO_007_01_2ug.raw --f C:\DIA-NN\1.8\2021MK017_EVBO_FCB\2021MK017_EVBO_008_01_2ug.raw --lib --threads 4 --verbose 1 *--out C:\DIA-NN\1.8\2021MK017-FCB\2021MK017-FCB.tsv* --qvalue 0.01 --matrices *--out-lib C:\DIA-NN\1.8\2021MK017-FCB\2021KM017-FCB-libr.tsv* --gen-spec-lib --predictor --fasta Z:\databases\canonical-dbs\2021_03\original_fastas\sp_human_2021_03.fasta --fasta-search --min-fr-mz 350 --max-fr-mz 1850 --met-excision --cut K*,R* --missed-cleavages 1 --min-pep-len 7 --max-pep-len 30 --min-pr-mz 500 --max-pr-mz 900 --min-pr-charge 1 --max-pr-charge 4 --unimod4 --var-mods 1 --var-mod UniMod:35,15.994915,M --var-mod UniMod:1,42.010565,*n --monitor-mod UniMod:1 --reanalyse --smart-profiling --pg-level 1 --peak-center --no-ifs-removal --relaxed-prot-inf