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ylab-hi / ScanNeo2

Snakemake-based computational workflow for neoantigen prediction from diverse sources
MIT License
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Request TESLA*fastq.gz #18

Closed nine-sarayut closed 1 month ago

nine-sarayut commented 2 months ago

From the .tests/integration/config_basic/config.yaml Do you know how I can get these files to test it? TESLA_9_2.fastq.gz TESLA_10_2.fastq.gz TESLA_11_2.fastq.gz

nttg8100 commented 1 month ago

TESLA is not published to use. Instead, you have to be a validated user at Synapse. Follow here: https://www.synapse.org/#!Synapse:syn21048999/wiki/603788 It is the only standard dataset.

riasc commented 1 month ago

Sorry for the late reply.

Thanks @nttg8100 for pointing this out. Yes, I cannot share this. You have to request the datasets.

I'm using this config file only for the linting. If you want to test it I will upload some test datasets and results. Let me get back to you on this.

riasc commented 1 month ago

Please have a look at https://github.com/ylab-hi/ScanNeo2/tree/main/.tests/integration for test files and example configs.

Feel free to open this again if you have additional questions. Thanks