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OpenOmics / chrom-seek

An awesome set of epigenetic pipelines for bulk cfChip-seq, ChIP-seq, and ATAC-seq
https://openomics.github.io/chrom-seek/
MIT License
5 stars 2 forks source link

Empty test files #20

Closed prc992 closed 1 year ago

prc992 commented 1 year ago

Hi,

I'm trying to test the pipeline using the test files but all files on https://github.com/OpenOmics/chrom-seek/tree/main/.tests are empty except the the peakcall.tsv and the contrasts.tsv. Can you have some working test files in the github?

Best

skchronicles commented 1 year ago

Hello @prc992,

Thank you for reaching out to us and for your interest in using the pipeline!

The fastq files in the .tests/ directory are being used on Github actions to dry-run the pipeline. They should not be used for any real analysis. Normal ChIP-seq & ATAC-seq data are typically a few GBs in size which is not suitable for version control platforms. If you are trying to find some test data sets, I would recommend downloading some data from GEO or SRA.

With that being said, the pipeline is currently set up to run on the NIH's Biowulf HPC cluster. At the current moment, we are working on making the pipeline more portable. You really need access to a high-performance computing cluster to efficiently process this type of data. Do you have a Biowulf account or an HPC account at an institute?

Please let me know what you think.

Best regards, Skyler Kuhn

skchronicles commented 1 year ago

Hey @prc992,

I ended up closing this issue due to inactivity. If so have any additional questions, please feel free to reach out to us here.

Have a great week, @skchronicles