Package: miso-tool
miso-toolTable of ContentsInstallationLicenseAboutThemiso-toolhelps you to parse the samples and sequencing runs info fromMISOPineryJSON files and generateNextflowsamplesheets, sample run info tables, and other useful files.InstallationInstall from PyPI usingpipwith:pip install miso-toolUsagemiso-tool --help

 Usage: miso-tool [OPTIONS]

 Parse the samples and sequencing runs info from MISO Pinery JSON files and generate Nextflow samplesheets and other files
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 By default, all samples are processed. Use --samples-list to specify a list of samples to process.

 ▌ NOTE: An Illumina Nextflow samplesheet.csv will only be generated if specified and if all Illumina runs have a SampleSheet.csv file that can be read. The output directory will contain the following files:

  • runs_without_rundir.txt: list of MISO run IDs without a corresponding run directory
  • all_sample_run_info.csv: table of all samples and their associated sequencing runs
  • original_to_clean_sample_id.txt: table of original sample IDs and their clean versions
  • nanopore_nextflow_samplesheet_{clean,original}.csv: Nextflow samplesheet for Nanopore runs with clean and original sample names
  • illumina_nextflow_samplesheet_{clean,original}.csv: Nextflow samplesheet for Illumina runs with clean and original sample names
  • sample_run_info.csv: table of user-specified samples and their associated sequencing runs

╭─ Options ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
│ *  --samples-json                   -s      PATH                             MISO Pinery Samples JSON file                                                                                                                                   │
│                                                                              [default: None]                                                                                                                                                 │
│                                                                              [required]                                                                                                                                                      │
│ *  --runs-json                      -r      PATH                             MISO Pinery Runs JSON file                                                                                                                                      │
│                                                                              [default: None]                                                                                                                                                 │
│                                                                              [required]                                                                                                                                                      │
│    --samples-list                   -l      PATH                             Samples to retrieve (one per line)                                                                                                                              │
│                                                                              [default: None]                                                                                                                                                 │
│    --outdir                         -o      PATH                             Output directory                                                                                                                                                │
│                                                                              [default: miso-tool-outdir]                                                                                                                                     │
│    --sample-run-info-csv            -S      PATH                             MISO Pinery Sample Run Info CSV file                                                                                                                            │
│                                                                              [default: None]                                                                                                                                                 │
│    --nanopore-nextflow-samplesheet  -N      PATH                             Nanopore Nextflow samplesheet                                                                                                                                   │
│                                                                              [default: None]                                                                                                                                                 │
│    --illumina-nextflow-samplesheet  -I      PATH                             Illumina Nextflow samplesheet                                                                                                                                   │
│                                                                              [default: None]                                                                                                                                                 │
│    --force                          -f                                       Overwrite existing files                                                                                                                                        │
│    --verbose                        -v                                                                                                                                                                                                       │
│    --version                        -V                                       Print 'gfflu version 0.0.2' and exit                                                                                                                            │
│    --install-completion                     [bash|zsh|fish|powershell|pwsh]  Install completion for the specified shell.                                                                                                                     │
│                                                                              [default: None]                                                                                                                                                 │
│    --show-completion                        [bash|zsh|fish|powershell|pwsh]  Show completion for the specified shell, to copy it or customize the installation.                                                                              │
│                                                                              [default: None]                                                                                                                                                 │
│    --help                                                                    Show this message and exit.                                                                                                                                     │
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 miso-tool version 0.0.2; Python 3.11.5Typical usage:miso-tool\--samples-json/path/to/samples.json\--runs-json/path/to/runs.json\--samples-list/path/to/samples.txt\--sample-run-info-csvsample-run-info.csv\--nanopore-nextflow-samplesheetnanopore-samplesheet.csv\--illumina-nextflow-samplesheetillumina-samplesheet.csv\--outdirmiso-tool-outdirLicensemiso-toolis distributed under the terms of theApache License 2.0.