conda activate scing

./build.sh

conda activate scing

./push.sh

$ cellranger --help
cellranger cellranger-7.0.0
Process 10x Genomics Gene Expression, Feature Barcode, and Immune Profiling data

USAGE:
    cellranger <SUBCOMMAND>

OPTIONS:
    -h, --help       Print help information
    -V, --version    Print version information

SUBCOMMANDS:
    count               Count gene expression (targeted or whole-transcriptome) and/or feature
                        barcode reads from a single sample and GEM well
    multi               Analyze multiplexed data or combined gene expression/immune
                        profiling/feature barcode data
    vdj                 Assembles single-cell VDJ receptor sequences from 10x Immune Profiling
                        libraries
    aggr                Aggregate data from multiple Cell Ranger runs
    reanalyze           Re-run secondary analysis (dimensionality reduction, clustering, etc)
    targeted-compare    Analyze targeted enrichment performance by comparing a targeted sample
                        to its cognate parent WTA sample (used as input for targeted gene
                        expression)
    targeted-depth      Estimate targeted read depth values (mean reads per cell) for a
                        specified input parent WTA sample and a target panel CSV file
    mkvdjref            Prepare a reference for use with CellRanger VDJ
    mkfastq             Run Illumina demultiplexer on sample sheets that contain 10x-specific
                        sample index sets
    testrun             Execute the 'count' pipeline on a small test dataset
    mat2csv             Convert a gene count matrix to CSV format
    mkref               Prepare a reference for use with 10x analysis software. Requires a GTF
                        and FASTA
    mkgtf               Filter a GTF file by attribute prior to creating a 10x reference
    upload              Upload analysis logs to 10x Genomics support
    sitecheck           Collect linux system configuration information
    help                Print this message or the help of the given subcommand(s)

$ cellranger count --help
cellranger-count
Count gene expression (targeted or whole-transcriptome) and/or feature barcode reads from a single
sample and GEM well

USAGE:
    cellranger count [OPTIONS] --id <ID> --transcriptome <PATH>

OPTIONS:
        --id <ID>
            A unique run id and output folder name [a-zA-Z0-9_-]+

        --description <TEXT>
            Sample description to embed in output files [default: ]

        --transcriptome <PATH>
            Path of folder containing 10x-compatible transcriptome reference

        --fastqs <PATH>
            Path to input FASTQ data

        --project <TEXT>
            Name of the project folder within a mkfastq or bcl2fastq-generated folder from which to
            pick FASTQs

        --sample <PREFIX>
            Prefix of the filenames of FASTQs to select

        --lanes <NUMS>
            Only use FASTQs from selected lanes

        --libraries <CSV>
            CSV file declaring input library data sources

        --feature-ref <CSV>
            Feature reference CSV file, declaring Feature Barcode constructs and associated barcodes

        --target-panel <CSV>
            The target panel CSV file declaring the target panel used, if any. Default analysis will
            exclude intronic mapped reads, which is the recommended mode for targeted assay. Use
            include-introns=true to include intronic mapped reads in analysis

        --expect-cells <NUM>
            Expected number of recovered cells, used as input to cell calling algorithm

        --force-cells <NUM>
            Force pipeline to use this number of cells, bypassing cell calling algorithm. [MINIMUM:
            10]

        --no-bam
            Set --no-bam to not generate the BAM file. This will reduce the total computation time
            for the pipestance and the size of the output directory. If unsure, we recommend not to
            use this option. BAM file could be useful for troubleshooting and downstream analysis

        --nosecondary
            Disable secondary analysis, e.g. clustering. Optional

        --r1-length <NUM>
            Hard trim the input Read 1 to this length before analysis

        --r2-length <NUM>
            Hard trim the input Read 2 to this length before analysis

        --include-introns <true|false>
            Include intronic reads in count (default=true unless --target-panel is specified in
            which case default=false)

        --chemistry <CHEM>
            Assay configuration. NOTE: by default the assay configuration is detected automatically,
            which is the recommened mode. You usually will not need to specify a chemistry. Options
            are: 'auto' for autodetection, 'threeprime' for Single Cell 3', 'fiveprime' for  Single
            Cell 5', 'SC3Pv1' or 'SC3Pv2' or 'SC3Pv3' for Single Cell 3' v1/v2/v3, 'SC3Pv3LT' for
            Single Cell 3' v3 LT, 'SC3Pv3HT' for Single Cell 3' v3 HT, 'SC5P-PE' or 'SC5P-R2' for
            Single Cell 5', paired-end/R2-only, 'SC-FB' for Single Cell Antibody-only 3' v2 or 5'
            [default: auto]

        --no-libraries
            Proceed with processing using a --feature-ref but no Feature Barcode libraries specified
            with the 'libraries' flag

        --check-library-compatibility <true|false>
            Whether to check for barcode compatibility between libraries. [default: true]

        --no-target-umi-filter
            Turn off the target UMI filtering subpipeline. Only applies when --target-panel is used

        --dry
            Do not execute the pipeline. Generate a pipeline invocation (.mro) file and stop

        --jobmode <MODE>
            Job manager to use. Valid options: local (default), sge, lsf, slurm or path to a
            .template file. Search for help on "Cluster Mode" at support.10xgenomics.com for more
            details on configuring the pipeline to use a compute cluster [default: local]

        --localcores <NUM>
            Set max cores the pipeline may request at one time. Only applies to local jobs

        --localmem <NUM>
            Set max GB the pipeline may request at one time. Only applies to local jobs

        --localvmem <NUM>
            Set max virtual address space in GB for the pipeline. Only applies to local jobs

        --mempercore <NUM>
            Reserve enough threads for each job to ensure enough memory will be available, assuming
            each core on your cluster has at least this much memory available. Only applies to
            cluster jobmodes

        --maxjobs <NUM>
            Set max jobs submitted to cluster at one time. Only applies to cluster jobmodes

        --jobinterval <NUM>
            Set delay between submitting jobs to cluster, in ms. Only applies to cluster jobmodes

        --overrides <PATH>
            The path to a JSON file that specifies stage-level overrides for cores and memory.
            Finer-grained than --localcores, --mempercore and --localmem. Consult
            https://support.10xgenomics.com/ for an example override file

        --uiport <PORT>
            Serve web UI at https://localhost:PORT

        --disable-ui
            Do not serve the web UI

        --noexit
            Keep web UI running after pipestance completes or fails

        --nopreflight
            Skip preflight checks

    -h, --help
            Print help information

$ cellranger vdj --help
cellranger-vdj
Assembles single-cell VDJ receptor sequences from 10x Immune Profiling libraries

USAGE:
    cellranger vdj [OPTIONS] --id <ID> --fastqs <PATH>

OPTIONS:
        --id <ID>
            A unique run id and output folder name [a-zA-Z0-9_-]+

        --description <TEXT>
            Sample description to embed in output files [default: ]

        --reference <PATH>
            Path of folder containing 10x-compatible VDJ reference. Optional if '--denovo' is
            specified

        --fastqs <PATH>
            Path to input FASTQ data

        --project <TEXT>
            Name of the project folder within a mkfastq or bcl2fastq-generated folder to pick FASTQs
            from

        --sample <PREFIX>
            Prefix of the filenames of FASTQs to select

        --lanes <NUMS>
            Only use FASTQs from selected lanes

        --denovo
            Run in reference-free mode (do not use annotations)

        --chain <CHAIN_SPEC>
            Chain type to display metrics for: 'TR' for T cell receptors, 'IG' for B cell receptors,
            or 'auto' to autodetect [default: auto]

        --inner-enrichment-primers <PATH>
            If inner enrichment primers other than those provided in the 10x kits are used, they
            need to be specified here as a textfile with one primer per line. Disable secondary
            analysis, e.g. clustering

        --dry
            Do not execute the pipeline. Generate a pipeline invocation (.mro) file and stop

        --jobmode <MODE>
            Job manager to use. Valid options: local (default), sge, lsf, slurm or path to a
            .template file. Search for help on "Cluster Mode" at support.10xgenomics.com for more
            details on configuring the pipeline to use a compute cluster [default: local]

        --localcores <NUM>
            Set max cores the pipeline may request at one time. Only applies to local jobs

        --localmem <NUM>
            Set max GB the pipeline may request at one time. Only applies to local jobs

        --localvmem <NUM>
            Set max virtual address space in GB for the pipeline. Only applies to local jobs

        --mempercore <NUM>
            Reserve enough threads for each job to ensure enough memory will be available, assuming
            each core on your cluster has at least this much memory available. Only applies to
            cluster jobmodes

        --maxjobs <NUM>
            Set max jobs submitted to cluster at one time. Only applies to cluster jobmodes

        --jobinterval <NUM>
            Set delay between submitting jobs to cluster, in ms. Only applies to cluster jobmodes

        --overrides <PATH>
            The path to a JSON file that specifies stage-level overrides for cores and memory.
            Finer-grained than --localcores, --mempercore and --localmem. Consult
            https://support.10xgenomics.com/ for an example override file

        --uiport <PORT>
            Serve web UI at https://localhost:PORT

        --disable-ui
            Do not serve the web UI

        --noexit
            Keep web UI running after pipestance completes or fails

        --nopreflight
            Skip preflight checks

    -h, --help
            Print help information