25-283.1

Description

Switched to raw_feature_bc_matrix instead of filtered one for GEX AnnData generation

25-283

Description

This release introduces a new step for pyCisTopic workflow. --attachGEX step converts GEX data (for multiome datasets only) to AnnData object and subsamples it to match ATAC data

Resolved issues

• Fixed and issue where you could not run intermediate step

Other changes

• Now peak metadata has it's own input argument called --pseudobulk_peaks

25-280

Description

This update aims to refactor the project's structure and resolved existing issues before a further expansion of the pipeline. Nf-core style is used for this project and all modules where aligned with this style to the best of my ability (and laziness).

Resolved issues

An issue #1 was resolved and a process to calculate barcode statistics (only number of fragments at this moment) was introduced. Moreover I removed the placeholder for fragments file name from both configs and pipeline inputs making pipeline to look for *fragments.tsv.gz file in specified directory instead.

Other changes

Other improvements were attempted:

• All parameters from pycistopic functions are now available for configuration by user
• Updated docker image and placed it to: link
• Improved outputs by changing structure (see README.md) and adding all intermediate pipeline outputs. Additionally versions.yml file is now outputted.

25-056

Overview

This is the first official release of the nf-atac pipeline, designed to process single-cell ATAC-seq (sc-ATAC and Multiome) data. This release includes only cisTopic for processing. This pipeline requires the data to have cell-type annotation to call peaks.

For more details on individual changes, you can refer to the commits.