Changelog

v2.1 (March 2025)

Minor update to support bigwig generation in MACS2 peak calling and to fix bugs

  • Updates to packages in the Conda environment

    • New dependencies added

    • Pre-existing dependencies updated

  • Snakefile updates

    • Rule chromsizes added to generate the .chromsizes file

    • Rule bigwig_signal added to generate .bigwig for MAC2-called peaks from input ATAC signal

    • Rule bigwig_noise added to generate .bigwig for MACS2-called local lambda values from control

    • Rule macs2 updated with the -B parameter, aiming to generate bedGraph files for MAC2-called peaks

  • config.yaml updates

    • fasta and chromsizes fields added to the macs2 section

    • Updates to the chooser section

      • Default resolutions narrowed

      • 1.0 replaced with 1 in the resolutions field

    • integrated_3, representing integrated gene activity, added to the groups field of the integration section

    • unintegrated_3 and integrated_3 added to the groups field of the diff_analysis section

  • Bugfix in workflow/chooser_aggr.Rmd

    • Aimed to fix an error that occurs when the boot::boot.ci function is called on an input vector with many ties, causing issues with smoothing resampling distributions in bootstrapping

    • Resolved by introducing very small random noise to the input vector

v2.0 (October 2024)

Major update to support Seurat v5

  • Package version updates

    • Upgraded Seurat from v4 to v5

    • Updated packages in Conda environments

    • Conda environments for the default Snakemake and ChooseR: env.yaml and workflow/chooser/env.yaml

  • Enhanced presentation of results in the report html files

  • config.yaml updates:
    • integrate field:

      • Removed n_dataset, reference, query. Instead, datasets will be split using the metadata column specified by the split_by key and then integrated.

      • Added integrate_method key to allow users to select the desired integration algorithm

    • coembed field: deprecated

    • cluster field: added detection_method to allow users to specify community detection algorithm.

    • weighted_nn field: added detection_method to allow users to specify community detection algorithm.

    • diff_analysis field: disabled logistic regression (LR) due to a bug causing unallocated CPU issues on HPC systems

    • guide field: deprecated

  • Bugfix: Resolved an issue with incorrect prefixes in clustering columns in the metadata (https://github.com/NICHD-BSPC/multiome-wf/issues/17)

v1.1, v1.2 (July 2024)

Minor update to upgrade package versions in the Conda environment and enhance functionality

  • Package version updates in the default Conda environment (env.yaml)

  • This update also fixes a clustering error caused by the Matrix package in R (https://github.com/NICHD-BSPC/multiome-wf/issues/18)

  • n_dataset key added to the integrate field in config.yaml. This key speficies the number of datasets to be integrated for cases where there are more than two datasets.

v1.0 (October 2023)

Major update to support Snakemake v7

  • Snakemake updates

    • Upgraded Snakemake from v6 to v7

    • Updated Snakefile to use the resources directive in each rule

    • Removed the --clusterconfig mechanism

    • Requires the use of a profile when running on a cluster (e.g. snakemake_profile prepared for NIH’s Biowulf)

    • Updated WRAPPER_SLURM accordingly

  • config.yaml updates
    • toydataset field

      • Added to optimize integration for small datasets

      • The toy_k key specifies the number of neighbors when weighting anchors during integration. This value is passed to the k.weight argument in Seurat’s IntegrateData function.

    • cluster field

      • Users are allowed to specify clustering resolution using the resolution key

      • Alternatively, dataset-optimized resolution can be used by setting the resolution key to null with chooseR.

v0.0 (March 2022)

Initial release on GitHub in March 2022