singjust/diann repository overview

$ docker run -it --rm -v `pwd`:/data/ singjust/diann:latest diann
DIA-NN 1.8.1 (Data-Independent Acquisition by Neural Networks)
Compiled on Apr 15 2022 08:45:18
Current date and time: Sat Jul 23 15:16:55 2022
Logical CPU cores: 12

0 files will be processed

$ docker run -it --rm -v `pwd`:/data/ singjust/diann:latest diann_to_openswath_format --help
Name: 
        Convert DIA-NN's Report file and XIC file to OpenSwaths SQLite osw and sqMass format

    Usage: 
        Rscript diann_to_openswath_format.R --[args] | --help

        Example: Rscript diann_to_openswath_format.R --diann_report_file=/data/diann_report.tsv --diann_xic_file=/data/diann_report.XIC.tsv --merged_osw_DB=TRUE --merged_sqmass_db=FALSE --outdir=/data/ --threads=1


    Options: 
        --diann_report_file: File path to DIANN report results file. *Required
        --diann_xic_file: File path to DIANN XIC tsv file. *Required
        --merged_osw_DB: Should a merged osw database be written out instead of individual runs. Default: TRUE
        --merged_sqmass_db: Should a merged sqMass database be written out instead of individual runs. Default: FALSE
        --outdir: Path to save sql sqMass databases. Default: getwd()
        --threads: The number of threads to use. This is only used if mergedDB is set to false, therefore, threading is used to create multiple files in parallel. Default: 1
        --verbose: Verbosity level for amount of console info. Has to be one of 0, 1, 2. Default: 1
        --help: Display this help message