How to create sample files
The files samples.tsv and units.tsv store all sample meta data needed to run pipelines that uses hydra-genetics.
These can be automatically generated from the .fastq-files by the hydra-genetics help tool.
Installation
Activate a python virtual environment. Then install the hydra-genetics tools using pip
source venv/bin/activate
pip install hydra_genetics
Usage
Create samples.tsv and units.tsv for all fastq files in a specified folder:
hydra-genetics create-input-files -d path/to/fastq-files/
Note
OBS! Sample names cannot include "_" (underscore)!
Options
| Option | Explanation |
|---|---|
| -d, --directory TEXT | path to dir where fastq-files should be looked for. Several folders can be specified by adding extra -d. [required] |
| -o, --outdir TEXT | Output directory for where rule will be added (default: current dir) |
| -p, --platform TEXT | Sequence platform that the data originate from, ex nextseq, miseq. Default Illumina |
| -t, --sample-type TEXT | Sample type, N |
| -s, --sample-regex TEXT | Regex used find fastq files and to extract sample from filename. Default '([A-Za-z0-9-]+)_.+.gz$' |
| -n, --read-number-regex TEXT | Regex used to extract read number from filename (note only number value). Default '_R([1-2]{1})_001' |
| -a, --adapters TEXT | Adapter sequence, comma separated |
| --post-file-modifier TEXT | Add string to output files |
| -f, --force | Overwrite existing files |
| -b, --default-barcode TEXT | Default barcode value that should be used when the fastq files are missing barcode information in their header, if not set the tool will fail if barcode can not be extracted |
| --tc FLOAT | Tumor content for all samples (default: 1.0) |
| --validate | See if fastq contain multiple runs/lanes by comparing first and last read. Note, will take time since whole file need to be parsed. |
| --ask | Ask user input when inconsistent machine id or flow cell id are found, only asked when --validate is set. |
| --th FLOAT | If occurences of a concesuns base in barcode is below this value a warning will be printed |
| --nreads INTEGER | Number of reads that will be used to generate consensus barcode. |
| --every INTEGER | Select every N reads for validation. |
| --help | Show help message and exit. |