Release notes

Version 2.1

2.1.1 July 18, 2022

  • Make cumulus workflow work with Cromwell v81+.

2.1.0 July 13, 2022

New Features:

  • Add CellBender workflow for ambient RNA removal.

  • CellRanger:

    • For ATAC-Seq data, add ARC-v1 chemistry keyword for analyzing only the ATAC part of 10x multiome data. See CellRanger scATAC-seq sample sheet section for details.
    • For antibody/hashing/citeseq/crispr data, add multiome chemistry keyword for the feature barcoding on 10x multiome data.

  • STARsolo:

    • In workflow output, besides mtx format gene-count matrices, the workflow also generates matrices in 10x-compatible hdf5 format.

Improvements:

  • CellRanger: For antibody/hashing/citeseq/crispr data,

    • cumulus_feature_barcoding v0.9.0+ now supports multi-threading and faster gzip file I/O.

  • Workflows check if output_directory is a valid Cloud URI based on the given backend value before execution. (Feature request #322 )

Updates:

  • Genome Reference:

  • Default version upgrade:

    • Update cellranger default to v7.0.0.
    • Update cellranger-atac default to v2.1.0.
    • Update cellranger-arc default to v2.0.1.
    • Update cumulus_feature_barcoding default to v0.10.0.
    • STARsolo workflow uses STAR v2.7.10a by default.

Version 2.0

2.0.0 March 14, 2022

Overall:

Workflow-specific:

  • Add STARsolo_create_reference workflow to build genome references for STARsolo counting. See its documentation for details.

  • On Cellranger workflow:

    • Add support for 10x Cell Ranger version 6.1.1 and 6.1.2, and use 6.1.2 by default. See Cell Ranger v6.1 release notes.
    • Add support for 10x Cell Ranger ARC version 2.0.1, and use it by default. See Cell Ranger ARC v2.0 release notes for the release notes.
    • Upgrade cumulus_feature_barcoding to version 0.7.0 to allow manually set barcode starting position (via input crispr_barcode_pos).
    • Add support for non 10x CRISPR assays. See the description of crispr DataType value in this section for details.
    • For input data consisting of fastq files, it’s able to handle folder structure of both flat (all fastq files in one folder) and nested (one subfolder per sample listed in the input sample sheet) forms.
    • Add fastq_outputs to workflow output, which contains mkfastq step output folders for samples listed in the input sample sheet.
    • Add count_outputs to workflow output, which contains count step output folderrs for samples listed in the input sample sheet.

  • On Spaceranger workflow:

    • Add support for 10x Space Ranger version 1.3.0 and 1.3.1, and use 1.3.1 by default. See Space Ranger v1.3 release notes for the release notes.

    • For input data consisting of fastq files, it’s able to handle folder structure of both flat (all fastq files in one folder) and nested (one subfolder per library) forms.

    • Add output section for the workflow. See here for details.

    • Retire old genome references:

      • Keep GRCh38-2020-A and mm10-2020-A.
      • Retire GRCh38, mm10, GRCh38-2020-A-premrna and mm10-2020-A-premrna. Users can still reach out to Cumulus team to ask for URIs to these old references, but they are not provided by default.

    • In the description of ReorientImages field of input sample sheet, add the information on its valid values.

  • On STARsolo workflow:

    • Add support for STAR version 2.7.9a, and use it by default. See STAR v2.7.9a release notes for the release notes.

    • Reorganize the workflow by exposing more inputs to users.

    • Add support on more protocols: 10x multiome, 10x 5’ (both SC5P-R2 and SC5P-PE), Slide-Seq and Share-Seq. See here <./starsolo.html#prepare-a-sample-sheet> for details.

    • Use input read1_fastq_pattern and read2_fastq_pattern to support fastq files generated by Cell Ranger or SeqWell, as well as Sequence Read Archive (SRA) data.

    • For input data consisting of fastq files, it’s able to handle folder structure of both flat (all fastq files in one folder) and nested (one subfolder per library) forms.

    • Do not attach filename prefix to output files to avoid the incorrect SJ raw feature.tsv symlink error, which would cause the folder delocalization fail. (see discussion with STAR team)

    • Add STAR log file to workflow output. This is the Log.out file if running STAR locally, which can be used for tracking the process and sharing with STAR team when opening an issue there.

    • Retire old genome references:

      • Keep GRCh38-2020-A, mm10-2020-A, and GRCh38-and-mm10-2020-A.
      • Retire old references listed here. Users can still reach out to Cumulus team to ask for URIs to them, but they are not provided by default.

  • On Demultiplexing workflow:

    • Upgrade demuxEM to version 0.1.7 for bug fix.

  • On Cellranger_create_reference workflow:

    • Add the generated reference file to the workflow output.
    • Bug fix in using input memory.
    • Update documentation to suggest only using Cell Ranger version 6.1.1 or later for building reference, as v6.0.1 has issues which leave the job running without terminating.

  • On Cellranger_atac_create_reference workflow:

    • Add the generated reference file to the workflow output.

  • On Cellranger_vdj_create_reference workflow:

    • Add the generated reference file to the workflow output.

Version 1.x

Version 1.5.1 September 15, 2021

  • Fix the issue of WDLs after Terra platform updates the Cromwell engine.

Version 1.5.0 July 20, 2021

  • On demultiplexing workflow
    • Update demuxEM to v0.1.6.
  • On cumulus workflow
    • Add Nonnegative Matrix Factorization (NMF) feature: run_nmf and nmf_n inputs.
    • Add integrative NMF (iNMF) data integration method: inmf option in correction_method input; the number of expected factors is also specified by nmf_n input.
    • When NMF or iNMF is enabled, word cloud plots and gene program UMAP plots of NMF/iNMF results will be generated.
    • Update Pegasus to v1.4.2.

Version 1.4.0 May 17, 2021

  • On cellranger workflow
    • Add support for multiomics analysis using linked samples, cellranger-arc count, cellranger multi and cellranger count will be automatically triggered based on the sample sheet
    • Add support for cellranger version 6.0.1 and 6.0.0
    • Add support for cellranger-arc version 2.0.0, 1.0.1, 1.0.0
    • Add support for cellranger-atac version 2.0.0
    • Add support for cumulus_feature_barcoding version 0.6.0, which handles CellPlex CMO tags
    • Add GRCh38-2020-A_arc_v2.0.0, mm10-2020-A_arc_v2.0.0, GRCh38-2020-A_arc_v1.0.0 and mm10-2020-A_arc_v1.0.0 references for cellranger-arc.
    • Fixed bugs in cellranger_atac_create_reference
    • Add delete undetermined FASTQs option for mkfastq
  • On demultiplexing workflow
    • Replace demuxlet with popscle, which includes both demuxlet and freemuxlet
  • On cumulus workflow
    • Fixed bug that remap_singlets and subset_singlets don’t work when input is in sample sheet format.
  • Modified workflows to remove trailing spaces and support spaces within output_directory

Version 1.3.0 February 2, 2021

  • On cumulus workflow:
    • Change cumulus_version to pegasus_version to avoid confusion.
    • Update to use Pegasus v1.3.0 for analysis.

Version 1.2.0 January 19, 2021

  • Add spaceranger workflow:
    • Wrap up spaceranger version 1.2.1
  • On cellranger workflow:
    • Fix workflow WDL to support both single index and dual index
    • Add support for cellranger version 5.0.1 and 5.0.0
    • Add support for targeted gene expression analysis
    • Add support for --include-introns and --no-bam options for cellranger count
    • Remove --force-cells option for cellranger vdj as noted in cellranger 5.0.0 release note
    • Add GRCh38_vdj_v5.0.0 and GRCm38_vdj_v5.0.0 references
  • Bug fix on cumulus workflow.
  • Reorganize the sidebar of Cumulus documentation website.

Version 1.1.0 December 28, 2020

  • On cumulus workflow:
    • Add CITE-Seq data analysis back. (See section Run CITE-Seq analysis for details)
    • Add doublet detection. (See infer_doublets, expected_doublet_rate, and doublet_cluster_attribute input fields)
    • For tSNE visualization, only support FIt-SNE algorithm. (see run_tsne and plot_tsne input fields)
    • Improve efficiency on log-normalization and DE tests.
    • Support multiple marker JSON files used in cell type annotation. (see organism input field)
    • More preset gene sets provided in gene score calculation. (see calc_signature_scores input field)
  • Add star_solo workflow (see STARsolo section for details):
    • Use STARsolo to generate count matrices from FASTQ files.
    • Support chemistry protocols such as 10X-V3, 10X-V2, DropSeq, and SeqWell.
  • Update the example of analyzing hashing and CITE-Seq data (see Example section) with the new workflows.
  • Bug fix.

Version 1.0.0 September 23, 2020

  • Add demultiplexing workflow for cell-hashing/nucleus-hashing/genetic-pooling analysis.
  • Add support on CellRanger version 4.0.0.
  • Update cumulus workflow with Pegasus version 1.0.0:
    • Use zarr file format to handle data, which has a better I/O performance in general.
    • Support focus analysis on Unimodal data, and appending other Unimodal data to it. (focus and append inputs in cluster step).
    • Quality-Control: Change percent_mito default from 10.0 to 20.0; by default remove bounds on UMIs (min_umis and max_umis inputs in cluster step).
    • Quality-Control: Automatically figure out name prefix of mitochondrial genes for GRCh38 and mm10 genome reference data.
    • Support signature / gene module score calculation. (calc_signature_scores input in cluster step)
    • Add Scanorama method to batch correction. (correction_method input in cluster step).
    • Calculate UMAP embedding by default, instead of FIt-SNE.
    • Differential Expression (DE) analysis: remove inputs mwu and auc as they are calculated by default. And cell-type annotation uses MWU test result by default.
  • Remove cumulus_subcluster workflow.

Version 0.x

Version 0.15.0 May 6, 2020

  • Update all workflows to OpenWDL version 1.0.
  • Cumulus now supports multi-job execution from Terra data table input.
  • Cumulus generates Cirrocumulus input in .cirro folder, instead of a huge .parquet file.

Version 0.14.0 February 28, 2020

  • Added support for gene-count matrices generation using alternative tools (STARsolo, Optimus, Salmon alevin, Kallisto BUStools).
  • Cumulus can process demultiplexed data with remapped singlets names and subset of singlets.
  • Update VDJ related inputs in Cellranger workflow.
  • SMART-Seq2 and Count workflows are in OpenWDL version 1.0.

Version 0.13.0 February 7, 2020

  • Added support for aggregating scATAC-seq samples.
  • Cumulus now accepts mtx format input.

Version 0.12.0 December 14, 2019

  • Added support for building references for sc/snRNA-seq, scATAC-seq, single-cell immune profiling, and SMART-Seq2 data.

Version 0.11.0 December 4, 2019

  • Reorganized Cumulus documentation.

Version 0.10.0 October 2, 2019

  • scCloud is renamed to Cumulus.
  • Cumulus can accept either a sample sheet or a single file.

Version 0.7.0 Feburary 14, 2019

  • Added support for 10x genomics scATAC assays.
  • scCloud runs FIt-SNE as default.

Version 0.6.0 January 31, 2019

  • Added support for 10x genomics V3 chemistry.
  • Added support for extracting feature matrix for Perturb-Seq data.
  • Added R script to convert output_name.seurat.h5ad to Seurat object. Now the raw.data slot stores filtered raw counts.
  • Added min_umis and max_umis to filter cells based on UMI counts.
  • Added QC plots and improved filtration spreadsheet.
  • Added support for plotting UMAP and FLE.
  • Now users can upload their JSON file to annotate cell types.
  • Improved documentation.
  • Added lightGBM based marker detection.

Version 0.5.0 November 18, 2018

  • Added support for plated-based SMART-Seq2 scRNA-Seq data.

Version 0.4.0 October 26, 2018

  • Added CITE-Seq module for analyzing CITE-Seq data.

Version 0.3.0 October 24, 2018

  • Added the demuxEM module for demultiplexing cell-hashing/nuclei-hashing data.

Version 0.2.0 October 19, 2018

  • Added support for V(D)J and CITE-Seq/cell-hashing/nuclei-hashing.

Version 0.1.0 July 27, 2018

  • KCO tools released!