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Recent Releases of https://github.com/alexslemonade/scpca-nf

https://github.com/alexslemonade/scpca-nf - scpca-nf v0.8.8

What's Changed

  • Use scpcaTools v0.4.3, which fixes a bug when setting the cell_id column in merged objects to now include both the library ID and the cell barcode (see https://github.com/AlexsLemonade/scpcaTools/releases/tag/v0.4.3).
  • Bug fix for https://github.com/AlexsLemonade/scpca-nf/issues/867

Full Changelog: https://github.com/AlexsLemonade/scpca-nf/compare/v0.8.7...v0.8.8

- R
Published by allyhawkins 7 months ago

https://github.com/alexslemonade/scpca-nf - scpca-nf v0.8.7

What's Changed

  • Bulk workflow now outputs both the raw counts and TPM
  • Define resource limits for individual processes
  • Updates to manifest and schema formatting
  • Addition of two new profiles - staging and production
  • Output a metrics JSON file
  • Processed and merged objects now contain a consensus cell type assignment
  • Bump to use scpcaTools:v0.4.2 which saves the assays in merged objects as sparse matrices rather than DelayedArray

Full Changelog: https://github.com/AlexsLemonade/scpca-nf/compare/v0.8.6...v0.8.7

- R
Published by allyhawkins 10 months ago

https://github.com/alexslemonade/scpca-nf - scpca-nf v0.8.6

What's Changed

  • merge.nf requires a minimum number of cells (3) for merging
  • Update GHA artifacts to v4
  • Added support for samples that are categorized as both a patient-derived xenograft and a cell line

Full Changelog: https://github.com/AlexsLemonade/scpca-nf/compare/v0.8.5...v0.8.6

- R
Published by allyhawkins about 1 year ago

https://github.com/alexslemonade/scpca-nf - scpca-nf v0.8.5

What's Changed

  • Use scpcaTools 0.4.1 images, which gives two major updates:
    • raw single-cell counts are rounded (as they were meant to be)
    • security updates with updated lightning in python packages that depend on it
  • converted use of deprecated addParams() to take for future Nextflow compatibility
  • correctly handle 2 cell case which does allow PCA creation

Full Changelog: https://github.com/AlexsLemonade/scpca-nf/compare/v0.8.4...v0.8.5

- R
Published by jashapiro over 1 year ago

https://github.com/alexslemonade/scpca-nf - scpca-nf v0.8.4

What's Changed

Bug fix release:

  • Only count single cell libraries for max merged
  • Account for different HVG name in merged object

Full Changelog: https://github.com/AlexsLemonade/scpca-nf/compare/v0.8.3...v0.8.4

- R
Published by jashapiro over 1 year ago

https://github.com/alexslemonade/scpca-nf - scpca-nf v0.8.3

What's Changed

  • Updates to AnnData objects:

    • PCA and UMAP embeddings are now stored as X_pca and X_umap (previously X_PCA and X_UMAP)
    • .var contains a highly_variable column indicating which genes are part of the list of highly variable genes
    • .uns contains a pca object with parameters and variance weights associated with the PCA embeddings

  • Addition of a max_merge_libraries parameter for merge.nf to limit the number of libraries that can be merged into a single object.

Full Changelog: https://github.com/AlexsLemonade/scpca-nf/compare/v0.8.2...v0.8.3

- R
Published by allyhawkins over 1 year ago

https://github.com/alexslemonade/scpca-nf - scpca-nf v0.8.2

What's Changed

  • Use new, slimmer scpcaTools docker containers (see https://github.com/AlexsLemonade/scpcaTools/releases/tag/v0.4.0)
  • Bulk files, bulk_quant.tsv and bulk_metadata.tsv, are now saved to a bulk directory
  • Main QC reports and cell type reports now include a table summarizing sample metadata (age, sex, diagnosis, etc.)

Full Changelog: https://github.com/AlexsLemonade/scpca-nf/compare/v0.8.1...v0.8.2

- R
Published by allyhawkins over 1 year ago

https://github.com/alexslemonade/scpca-nf - scpca-nf v0.8.1

What's Changed

  • Output HDF5 files now have the .h5ad extension instead of .hdf5
  • Bug fixes:
    • Skip running CellAssign if a processed object only has 1 cell
    • No cell type reports are created if processed objects only have 1 cell
    • Make sure to account for no genetic demultiplexing when estimating sample cell counts for metadata.json
    • Skip any downstream processing if no cells are left after filtering out empty droplets

Full Changelog: https://github.com/AlexsLemonade/scpca-nf/compare/v0.8.0...v0.8.1

- R
Published by allyhawkins almost 2 years ago

https://github.com/alexslemonade/scpca-nf - scpca-nf v0.8.1

What's Changed

  • Output HDF5 files now have the .h5ad extension instead of .hdf5
  • Bug fixes:
    • Skip running CellAssign if a processed object only has 1 cell
    • No cell type reports are created if processed objects only have 1 cell
    • Make sure to account for no genetic demultiplexing when estimating sample cell counts for metadata.json
    • Skip any downstream processing if no cells are left after filtering out empty droplets

Full Changelog: https://github.com/AlexsLemonade/scpca-nf/compare/v0.8.0...v0.8.1

- R
Published by allyhawkins almost 2 years ago

https://github.com/alexslemonade/scpca-nf - scpca-nf v0.8.0

What's Changed

  • Addition of merge.nf used to create merged SingleCellExperiment and AnnData objects
    • The merged workflow takes as input a list of projects and creates a single merged object for each project
    • Also includes a report, summarizing the contents of the merged object
  • Some minor aesthetic fixes to cell type report
  • Use bz2 compression to reduce file sizes for SingleCellExperiment objects
  • Add nextflow_schema.json to repo

Full Changelog: https://github.com/AlexsLemonade/scpca-nf/compare/v0.7.3...v0.8.0

- R
Published by allyhawkins almost 2 years ago

https://github.com/alexslemonade/scpca-nf - scpca-nf v0.8.0

What's Changed

  • Addition of merge.nf used to create merged SingleCellExperiment and AnnData objects
    • The merged workflow takes as input a list of projects and creates a single merged object for each project
    • Also includes a report, summarizing the contents of the merged object
  • Some minor aesthetic fixes to cell type report
  • Use bz2 compression to reduce file sizes for SingleCellExperiment objects
  • Add nextflow_schema.json to repo

Full Changelog: https://github.com/AlexsLemonade/scpca-nf/compare/v0.7.3...v0.8.0

- R
Published by allyhawkins almost 2 years ago

https://github.com/alexslemonade/scpca-nf - scpca-nf v0.7.3

What's Changed

  • Skip any additional processing (clustering, cell type assignment) for processed objects with 0 cells
  • Use new max_mem label for CellAssign classification, which uses params.max_memory after the first failure.

Full Changelog: https://github.com/AlexsLemonade/scpca-nf/compare/v0.7.2...v0.7.3

- R
Published by allyhawkins almost 2 years ago

https://github.com/alexslemonade/scpca-nf - scpca-nf v0.7.2

What's Changed

  • Skip CellAssign if too few cells
  • Small bug fixes for running multiplexed samples through cell typing
  • Skip cell typing for cell line samples
  • Small adjustments to UMAPs in the cell typing report
  • Account for missing input files

Full Changelog: https://github.com/AlexsLemonade/scpca-nf/compare/v0.7.1...v0.7.2

- R
Published by allyhawkins about 2 years ago

https://github.com/alexslemonade/scpca-nf - scpca-nf v0.7.1

What's Changed

  • Update memory and CPU requests for running CellAssign
  • Set max retries after AWS instance failure to 2
  • Use On Demand instances on 3rd retry
  • Create faceted UMAPs in cell type report

Full Changelog: https://github.com/AlexsLemonade/scpca-nf/compare/v0.7.0...v0.7.1

- R
Published by allyhawkins about 2 years ago

https://github.com/alexslemonade/scpca-nf - scpca-nf v0.7.0

What's Changed

  • Addition of cell type annotation to the main workflow, including:
    • Annotation with either SingleR or CellAssign
    • New output that includes a processed SingleCellExperiment and AnnData objects with cell type annotations and a cell type summary report
    • Documentation for adding cell type annotations
  • By default, cell type annotation is turned off. To run the workflow with cell type annotation, use the --perform_celltyping flag.
  • By default, if cell typing results already exist, previous results are used. The --repeat_celltyping flag can be used to repeat previous cell type annotation.
  • Addition of pre-commit to the repo

Full Changelog: https://github.com/AlexsLemonade/scpca-nf/compare/v0.6.3...v0.7.0

- R
Published by allyhawkins about 2 years ago

https://github.com/alexslemonade/scpca-nf - scpca-nf v0.6.3

What's Changed

  • Make sure all RDS files are compressed
  • Accommodate running multiple projects at once using the --project parameter

Full Changelog: https://github.com/AlexsLemonade/scpca-nf/compare/v0.6.2...v0.6.3

- R
Published by allyhawkins over 2 years ago

https://github.com/alexslemonade/scpca-nf - scpca-nf v0.6.2

What's Changed

  • Fixes a bug to make sure there's at least one gene or feature in the SingleCellExperiment object prior to converting to AnnData objects
  • Temporarily remove cell type section from main qc report

Full Changelog: https://github.com/AlexsLemonade/scpca-nf/compare/v0.6.1...v0.6.2

- R
Published by allyhawkins over 2 years ago

https://github.com/alexslemonade/scpca-nf - scpca-nf v0.6.2

What's Changed

  • Fixes a bug to make sure there's at least one gene or feature in the SingleCellExperiment object prior to converting to AnnData objects

Full Changelog: https://github.com/AlexsLemonade/scpca-nf/compare/v0.6.1...v0.6.2

- R
Published by allyhawkins over 2 years ago

https://github.com/alexslemonade/scpca-nf - scpca-nf v0.6.1

What's Changed

  • Fixes a bug when handling NA values in library metadata

Full Changelog: https://github.com/AlexsLemonade/scpca-nf/compare/v0.6.0...v0.6.1

- R
Published by allyhawkins over 2 years ago

https://github.com/alexslemonade/scpca-nf - scpca-nf v0.6.0

What's Changed

  • Add cluster assignments to processed SingleCellExperiment object
  • Incorporate sample metadata into SingleCellExperiment objects
  • Export all SingleCellExperiment objects as AnnData objects
  • Added a workflow for generating references for cell type annotation
  • Added CellAssign to cell type annotation
  • Initial cell type report additions
  • Allow for addition of submitter cell types
  • Add style guide
  • Account for failures in modeling gene variance and PCA

Full Changelog: https://github.com/AlexsLemonade/scpca-nf/compare/v0.5.4...v0.6.0

- R
Published by allyhawkins over 2 years ago

https://github.com/alexslemonade/scpca-nf - scpca-nf v0.5.4

What's Changed

  • Error handling for modeling gene variance, calculating PCA, and calculating UMAP

Full Changelog: https://github.com/AlexsLemonade/scpca-nf/compare/v0.5.3...v0.5.4

- R
Published by allyhawkins over 2 years ago

https://github.com/alexslemonade/scpca-nf - scpca-nf v0.5.3

What's Changed

  • Fixed intermittent ADT filtering bug
  • Improved memory usage for QC report

Full Changelog: https://github.com/AlexsLemonade/scpca-nf/compare/v0.5.2...v0.5.3

- R
Published by sjspielman over 2 years ago

https://github.com/alexslemonade/scpca-nf - scpca-nf v0.5.2

What's Changed

  • Added post-processing (filtering and normalization) for antibody-derived tag (ADT) data from CITE-seq experiments
  • Added support for using additional organisms as references
  • QC report updates
  • Workflow development updates:
    • Improved behavior in limited resource environments
    • Added more workflow testing with stub blocks
  • Experimental features added:
    • Integration of multiple samples
    • Cell-type annotation

Full Changelog: https://github.com/AlexsLemonade/scpca-nf/compare/v0.5.1...v0.5.2

- R
Published by sjspielman over 2 years ago

https://github.com/alexslemonade/scpca-nf - scpca-nf v0.5.1

What's Changed

  • Make genetic demultiplexing optional

Full Changelog: https://github.com/AlexsLemonade/scpca-nf/compare/v0.5.0...v0.5.1

- R
Published by allyhawkins over 2 years ago

https://github.com/alexslemonade/scpca-nf - scpca-nf v0.5.0

What's Changed

  • Added support for processing libraries from multiple organisms
  • Available references for mapping now include Human and Mouse Ensembl v104
  • Option to skip feature mapping if already done
  • Publish checkpoints for feature mapping

Full Changelog: https://github.com/AlexsLemonade/scpca-nf/compare/v0.4.2...v0.5.0

- R
Published by allyhawkins almost 3 years ago

https://github.com/alexslemonade/scpca-nf - scpca-nf v0.4.2

What's Changed

  • Updated URL
  • Ensure feature barcode files provided to salmon index contain the correct columns

Full Changelog: https://github.com/AlexsLemonade/scpca-nf/compare/v0.4.1...v0.4.2

- R
Published by sjspielman almost 3 years ago

https://github.com/alexslemonade/scpca-nf - scpca-nf v0.4.1

What's Changed

  • Catch errors in UMAP calculation in post_process_sce.R
  • Update to use scpcaTools v0.2.1

Full Changelog: https://github.com/AlexsLemonade/scpca-nf/compare/v0.4.0...v0.4.1

- R
Published by allyhawkins about 3 years ago

https://github.com/alexslemonade/scpca-nf - scpca-nf v0.4.0

What's Changed

  • Addition of filtering, normalization, and dimensionality reduction of SingleCellExperiment objects
  • Tracking of metadata at checkpoints
  • Add script for downloading local reference files and images
  • Add instructions for downloading local reference files
  • Use scpcaTools v0.2.0 including updates to reading in alevin-fry data with fishpond::loadFry()
  • Reorganization of documentation

Full Changelog: https://github.com/AlexsLemonade/scpca-nf/compare/v0.3.4...v0.4.0

- R
Published by allyhawkins about 3 years ago

https://github.com/alexslemonade/scpca-nf - scpca-nf v0.3.4

What's Changed

This release fixes a few bugs and errors that we have seen when running on external systems. Thank you to testers for helping uncover these!

  • Fix for potentially missing (unneeded) multiplex pool file in https://github.com/AlexsLemonade/scpca-nf/pull/201
  • Make scripts executable in https://github.com/AlexsLemonade/scpca-nf/pull/202
  • add AWS anonymous access to example config for easier running on external systems https://github.com/AlexsLemonade/scpca-nf/pull/206

Full Changelog: https://github.com/AlexsLemonade/scpca-nf/compare/v0.3.3...v0.3.4

- R
Published by jashapiro over 3 years ago

https://github.com/alexslemonade/scpca-nf - scpca-nf v0.3.3

What's Changed

  • Update from scpcaTools v0.1.7 to v0.1.8
    • includes special handling of libraries with one sample and cell hashing in the QC report
  • Skips demultiplexing for libraries with cell hashing, but only containing one sample

Full Changelog: https://github.com/AlexsLemonade/scpca-nf/compare/v0.3.2...v0.3.3

- R
Published by allyhawkins over 3 years ago

https://github.com/alexslemonade/scpca-nf - scpca-nf v0.3.2

What's Changed

  • Update from scpcaTools v0.1.6 to v0.1.7
    • includes the addition of a section in the QC report specifically for multiplexed libraries

Full Changelog: https://github.com/AlexsLemonade/scpca-nf/compare/v0.3.1...v0.3.2

- R
Published by allyhawkins over 3 years ago

https://github.com/alexslemonade/scpca-nf - scpca-nf v0.3.1

What's Changed

  • Update Alevin-fry to 0.5.0 and Salmon to 0.8.0
  • Improved error handling for miQC failures
  • Change the default queue to use a larger disk after the first job failure
  • Addition of a new profile that uses an autoscaling EBS

Full Changelog: https://github.com/AlexsLemonade/scpca-nf/compare/v0.3.0...v0.3.1

- R
Published by allyhawkins over 3 years ago

https://github.com/alexslemonade/scpca-nf - scpca-nf v0.3.0

What's Changed

  • Initial support for multiplexed libraries
    • Addition of a genetic demultiplexing workflow using cellsnp/vireo
    • Report demultiplexing results based on cellhash data
  • Updates to user instructions and example metadata

Full Changelog: https://github.com/AlexsLemonade/scpca-nf/compare/v0.2.7...v0.3.0

- R
Published by allyhawkins almost 4 years ago

https://github.com/alexslemonade/scpca-nf - scpca-nf v0.2.7

What's Changed

  • Output of the spatial transcriptomics workflow now includes the <library_id>_metadata.json file nested inside the <library_id>_spatial folder

Full Changelog: https://github.com/AlexsLemonade/scpca-nf/compare/v0.2.6...v0.2.7

- R
Published by allyhawkins almost 4 years ago

https://github.com/alexslemonade/scpca-nf - scpca-nf v0.2.6

What's Changed

  • small bug fix in spaceranger workflow to ensure index name is present in the metadata file, even when spaceranger process is skipped

Full Changelog: https://github.com/AlexsLemonade/scpca-nf/compare/v0.2.5...v0.2.6

- R
Published by allyhawkins almost 4 years ago

https://github.com/alexslemonade/scpca-nf - scpca-nf v0.2.5

What's Changed

  • Added option to skip spaceranger quantification for spatial workflow using the --repeat_mapping flag
  • Reorganized structure of spaceranger output files
  • Added a ccdl profile

Full Changelog: https://github.com/AlexsLemonade/scpca-nf/compare/v0.2.4...v0.2.5

- R
Published by allyhawkins almost 4 years ago

https://github.com/alexslemonade/scpca-nf - v0.2.4

What's Changed

  • Split process settings from AWS profile
  • Add minimal parameter checks & manifest
  • Add template config for external users
  • Add instructions for external users to README

Full Changelog: https://github.com/AlexsLemonade/scpca-nf/compare/v0.2.3...v0.2.4

- R
Published by jashapiro almost 4 years ago

https://github.com/alexslemonade/scpca-nf - scpca-nf v0.2.3

What's Changed

  • Increase maximum retry attempts from 2x to 3x

Full Changelog: https://github.com/AlexsLemonade/scpca-nf/compare/v0.2.0...v0.2.3

- R
Published by allyhawkins about 4 years ago

https://github.com/alexslemonade/scpca-nf - scpca-nf v0.2.2

What's Changed

  • Increase memory request for fastp for bulk RNA-seq workflow to accommodate larger libraries
  • Double memory request on every retry attempt

Full Changelog: https://github.com/AlexsLemonade/scpca-nf/compare/v0.2.0...v0.2.2

- R
Published by allyhawkins about 4 years ago

https://github.com/alexslemonade/scpca-nf - scpca-nf v0.2.1

What's Changed

  • Split up CPU and memory handling with labels
  • Updates to error handling with cell filtering with the addition of scpcaTools 0.1.4
  • Add filtering method to metadata.json

Full Changelog: https://github.com/AlexsLemonade/scpca-nf/compare/v0.2.0...v0.2.1

- R
Published by jashapiro about 4 years ago

https://github.com/alexslemonade/scpca-nf - scpca-nf 0.2.0

What's Changed

  • Skips repeated mapping steps by default for bulk and single-cell RNA-seq data
    • use --repeat_mapping flag to force remapping
  • Remove implicit dependence on S3 for file locations
  • Moved index and barcode defaults to public reference bucket
  • Add bulk RNA-seq metadata file for each project
  • Update to scpcaTools 0.1.3
    • Rounds expression counts for single-cell data

Full Changelog: https://github.com/AlexsLemonade/scpca-nf/compare/v0.1.3...v0.2.0

- R
Published by jashapiro about 4 years ago

https://github.com/alexslemonade/scpca-nf - scpca-nf 0.1.3

What's Changed

  • Add bulk RNA-seq processing with salmon
  • Add spatial expression analysis with Space Ranger
  • Memory and disk space updates for large samples
  • Reorganize configuration files and parameters
  • Update workflow to use scpcaTools 0.1.2 (changes filtering to use emptyDropsCellRanger)

Full Changelog: https://github.com/AlexsLemonade/scpca-nf/compare/v0.1.2...v0.1.3

- R
Published by jashapiro about 4 years ago

https://github.com/alexslemonade/scpca-nf - scpca-nf 0.1.2

Changes:

  • Change to use cr-like-em for default alevin-fry resolution NOTE
  • Reduce default memory usage

- R
Published by jashapiro over 4 years ago

https://github.com/alexslemonade/scpca-nf - scpca-nf 0.1.1

Changes:

  • takes advantage of changes in scpcaTools 0.1.1 for more robust handling of miQC model fit failures.

- R
Published by jashapiro over 4 years ago

https://github.com/alexslemonade/scpca-nf - Initial workflow release

This is the initial release of the scpca-nf workflow. To run this version, use:

nextflow run AlexsLemonade/scpca-nf -r v0.1.0 -profile batch --project <PROJID> --outdir <s3://bucket/prefix>`

or similar, where <PROJID> is the project ID for which you want to run all samples and <s3://bucket/prefix> is the bucket & prefix to which output files will be written.

- R
Published by jashapiro over 4 years ago