A tool to work with sequencing run and sample info from MISO LIMS Pinery JSON data
Project description
miso-tool
Table of Contents
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 0.0.2' 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. │
╰──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
miso-tool version 0.0.2; 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.
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