miso-tool 0.0.1

A tool to work with sequencing run and sample info from MISO LIMS Pinery JSON data

miso-tool

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Table of Contents

• Installation
• License

About

The miso-tool helps you to parse the samples and sequencing runs info from MISO Pinery JSON files and generate Nextflow samplesheets, sample run info tables, and other useful files.

Installation

Install from PyPI using pip with:

pip install miso-tool

Usage

miso-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
 ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
 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 0.0.1' 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.                                                                                                                                     │
╰──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯

 miso-tool version 0.0.1; Python 3.11.5

Typical usage:

miso-tool \
  --samples-json /path/to/samples.json \
  --runs-json /path/to/runs.json \
  --samples-list /path/to/samples.txt \
  --sample-run-info-csv sample-run-info.csv \
  --nanopore-nextflow-samplesheet nanopore-samplesheet.csv \
  --illumina-nextflow-samplesheet illumina-samplesheet.csv \
  --outdir miso-tool-outdir

License

miso-tool is distributed under the terms of the Apache License 2.0.