elembio/cells2stats repository overview

Usage: cells2stats [OPTIONS] RUN_DIRECTORY

positional arguments:
        RUN_DIRECTORY               Location of run directory

optional arguments:
        --bases2fastq, -B PATH          Path to bases2fastq binary used for fastq generation during OPS analysis [bases2fastq]
        --batch, -b BATCH               Restrict analysis to batch(es) that match comma delimited list (e.g. -b B01,B02,B03)
        --bowtie PATH                   Path to bowtie (v1) binary used in OPS analysis [bowtie]
        --bowtie-build PATH             Path to bowtie-build binary used in OPS analysis [bowtie-build]
        --cellprofiler, -c PATH         Path to cellprofiler utility
        --error-on-missing, -m          Terminate execution for a missing file. By default, missing files are skipped and execution continues
        --help, -h                      Print usage statement and exit
        --input-remote, -i REMOTE       Rclone remote name for remote RUN_DIRECTORY
        --log-level, -l LEVEL           Minimum log level [info] (debug, info, warning, or error)
        --max-unassigned, -u MAX        Limit to the number of unassigned sequences to report. [30], (1-10,000)
        --no-error-on-invalid, -n       Skip invalid files and continue execution. By default, execution is terminated for an invalid file
        --num-threads, -j THREADS       Number of threads [1]
        --output, -o DIRECTORY          Location to save output [RUN_DIRECTORY/Cytoprofiling/<timestamp>]
        --output-remote, -r REMOTE      Rclone remote name for remote OUTPUT_DIRECTORY
        --panel, -p PANEL               Local or remote path to panel JSON
        --python, -P PATH               Path to python executable used for visualization script [/usr/bin/python3]
        --run-manifest, -R MANIFEST     Local or remote path to run manifest. Must have extension .csv or .json
        --samtools PATH                 Path to samtools binary used in OPS analysis [samtools]
        --segmentation, -S PATH         Custom cell segmentation directory
        --skip-cellprofiler, -s         Skip execution of cellprofiler
        --skip-html-report, -H          Skip generation of MultiQC HTML report
        --tca-manifest, -M              Local or remote path to target cell assignment manifest. Must have extension .csv or .json
        --tile, -t REGEX                Restrict analysis to tiles that match REGEX
        --verbose-transfer, -T          For remote transfers, print to stdout the name of every file downloaded/uploaded
        --version, -v                   Display cells2stats version and exit
        --visualization, -V             Generate files for visualization for all tiles (ignores tile/well filters)
        --visualization-only, -O        Generate files for visualization as with -V, but skip all other stats
        --well, -w WELL                 Restrict analysis to well location(s) that match comma delimited list (e.g. -w A1,A2,B2)