Usage
Checks integrity of sequencing files (FASTQ, BAM).
Use --fastq-paired for paired-end FASTQ, --fastq-single for single-end FASTQ, --bam for BAM files, or --raw for only calculating checksums of any file. These flags can be used multiple times.
By default, the tool will exit immediately after the first error is found. Use --continue-on-error to check all files regardless of errors.
Usage: grz-check [OPTIONS] --output <OUTPUT>
Options:
--show-progress <SHOW_PROGRESS>
Flag to show progress bars during processing
[possible values: true, false]
--fastq-paired <FQ1_PATH> <FQ2_PATH> <FQ1_READ_LEN> <FQ2_READ_LEN>
A paired-end FASTQ sample. Provide FQ1, FQ2, FQ1 read length, and FQ2 read length. Read Length: >0 for fixed, 0 for auto-detect, <0 to skip length check
--fastq-single <FQ_PATH> <READ_LEN>
A single-end FASTQ sample. Provide the file path and read length. Read Length: >0 for fixed, 0 for auto-detect, <0 to skip length check
--bam <BAM_PATH>
A single BAM file to validate
--raw <FILE_PATH>
A file for which to only calculate the SHA256 checksum, skipping all other validation
--output <OUTPUT>
Path to write the output JSONL report
--continue-on-error
Continue processing all files even if an error is found
--threads <THREADS>
Number of threads to use for processing
-h, --help
Print help (see a summary with '-h')
-V, --version
Print version
Example
# --fastq-paired R1 R2 read_length_R1 read_length_R2
# --fastq-single R1 read_length_R1
grz-check --show-progress --output report.jsonl --fastq-paired path/to/sample__R1.fastq.gz path/to/sample_R2.fastq.gz 150 150 --fastq-single path/to/sample.fastq.gz 151
1 maintainer
Metadata
1 maintainer
Release files for grz-check 0.4.0
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Source distribution (sdist)
| File | Size | Uploaded | Provenance | |
|---|---|---|---|---|
| grz_check-0.4.0.tar.gz | 33.9 kB | With provenance | Details |
Built distributions (wheels)
Total release size: 7.4 MB
Release files / grz_check-0.4.0.tar.gz
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| Size | 33.9 kB |
| Tags | Source |
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