3.0.0

• Overall highlights:
  • For data localization/delocalization on GCP, now use gcloud storage commands instead of gsutil, as gsutil is deprecated, and gcloud storage achieves some speed improvement.
  • Users no longer need to specify backend input for AWS or local backend, and it is now automatically figured out from output_directory location.
  • Remove support on mkfastq in Cellranger and Spaceranger workflows, as it will soon be removed from Cell Ranger and Space Ranger. Users need to run BCL Convert themselves first to generate FASTQ data.
  • For Cellranger and Spaceranger workflows, provide better support for shared computing environments like AWS Batch, GCP Batch and sHPC.
  • For resources like prebuilt references, they are now held in a single-region bucket gs://cumulus-ref in US-CENTRAL1 to reduce potentially higher network cost at users’ side from the previous multi-region bucket.
• Cellranger workflow:
  • Upgrade cellranger_version default to 9.0.1.
  • Remove mkfastq related workflow inputs.
  • Remove run_count input as it’s always true.
  • Support input data format as a TAR file containing FASTQ files.
  • Change FeatureBarcodeFile column header to AuxFile (for backward compatibility, FeatureBarcodeFile is still accepted but not recommended).
  • Support all the 3 Sample Multiplexing methods provided since Cell Ranger v9.0. See details.
  • For single-cell and single-nucleus RNA-seq:
    • Add new genome reference mRatBN7.2-2024-A
    • Remove Target Gene Expression-related inputs, as it’s no longer supported since Cell Ranger v7.2.0.
  • For feature barcoding:
    • Upgrade cumulus_feature_barcoding_version to 1.0.0.
    • The workflow now can automatically detect the chemistry type of the data:
      • auto by default: The workflow checks all possible assay types to decide the correct one.
      • threeprime: The workflow checks all 3’ assay types to decide the correct one.
      • fiveprime: The workflow checks all 5’ assay types to decide the correct one.
    • Reorg the keywords in Chemistry column of sample sheet: 5’ now only has 2 types, SC5Pv2 and SC5Pv3 for 5’ v2 and v3 chemistries where only R2 is used for alignment.
    • Support the new format of 10x cell barcode inclusion lists provided in Cell Ranger v9.0+.
    • Fix issue in processing UTF-encoded feature barcode files
  • For immune profiling:
    • Add types vdj_t, vdj_b and vdj_t_gd for DataType column. See 10x 5’ Immune Profiling Kit for details.
    • Remove chain input, as it is now automatically decided by user-specified DataType types.
    • For vdj_t_gd type samples, support the feature of specifying primer sequences used to enrich cDNA for V(D)J sequences. To enable it, provide a .txt file in AuxFile column of the sample, and it will be passed to --inner-enrichment-primers option of cellranger vdj in execution.
  • For Flex Gene Expression:
    • Remove ProbeSet column. The probe set is now automatically decided based on user-specified Reference name.
    • Support Flex probe sets v1.1 which are associated with 2024-A genome references.
  • For CellPlex using CMO:
    • Remove cmo_set input. If using custom CMOs in your experiment, just provide the custom feature reference file in AuxFile column of the cmo type sample.
• Spaceranger workflow:
  • Upgrade spaceranger_version default to 3.1.3.
  • Remove mkfastq related workflow inputs.
  • Remove run_count input as it’s always true.
  • Remove support on Targeted Gene Expression analysis, as it’s no longer supported since Space Ranger v2.1.1.

2.6.3

This is a small bug-fix version bump:

• Update Demultiplexing workflow to work with Stratocumulus v0.2.4

2.6.2

In Cellranger workflow:

• cellranger_arc_version default is "2.0.2.strato" , which works with workflow v2.6.1 or later.
• If using "2.0.2", make sure to use workflow v2.6.0 or earlier.
• Set to "2.0.2.custom-max-cell" if analyzing 10x multiome data with increased max cell threshold which is 80,000 in this version. Notice that this version also only work with workflow v2.6.1 or later.

2.6.1

• In Cellranger workflow: Add new genome references for single-cell/nucleus RNA-Seq: GRCh38-2024-A for human, GRCm39-2024-A for mouse, and GRCh38_and_GRCm39-2024-A for human and mouse.
• In Spaceranger workflow: Add a new probe set mouse_probe_v2 for mouse.
• Some underlying workflow improvement.

2.6.0

Update:

• In Cellranger workflow:
  • Upgrade cellranger_version default to 8.0.0.
  • Upgrade cumulus_feature_barcoding version default to 0.11.3.
• In Spaceranger workflow:
  • Upgrade spaceranger_version default to 3.0.0.
  • Support Visium HD data.

2.5.0

Improvements

• In Cellranger workflow:
  • Add multi_disk_space input for specifying disk size used by Fixed RNA Profiling or 10x multiome jobs, which usually take large amount.
• In Cellbender workflow:
  • With 0.3.0 default Cell Bender version, users don’t need to always specify expected_cells or total_droplets_included input.

Updates

• In Cellranger workflow:
  • Upgrade cellranger_version default to 7.2.0.
  • Upgrade cumulus_feature_barcoding version default to 0.11.2.
  • Add GRCh38 VDJ v7.1.0 reference: GRCh38_vdj_v7.1.0.
• In Spaceranger workflow:
  • Upgrade spaceranger_version default to 2.1.1.
• In Demultiplexing workflow:
  • Upgrade souporcell_version default to 2.5.
• In Cellbender workflow:
  • Upgrade cellbender_version default to 0.3.0.

2.4.1

Improve

• In Cellranger workflow:
  • Fixed RNA Profiling now accepts custom probe set references (#381 by @yihming )
• In STARsolo workflow:
  • Add limitBAMsortRAM and outBAMsortingBinsN inputs to handle out-of-memory error in BAM sorting phase. (#375 by @yihming )
• In GeoMx_fastq_to_dcc workflow:
  • Support multiple FASTQ folders as input. (#380 by @joshua-gould )

Updates

• In Demultiplexing workflow:
  • Upgrade souporcell_version to 2022.12, which is based on commit 9fb527 on 2022/12/13. (#376 by @yihming )
• In STARsolo workflow:
  • Upgrade star_version to 2.7.10b. (#379 by @yihming )

Bug Fixes

• In Spaceranger workflow:
  • Fix the image localization issue for CytAssist samples. (#382 by @yihming )

2.4.0

• In Cellranger workflow:
  • Upgrade cellranger_version default to 7.1.0.
  • Add Mouse probe set v1.0 for Fixed RNA Profiling analysis.
  • Add probe set v1.0.1 of both Human and Mouse for Fixed RNA Profiling analysis.
  • Upgrade cumulus_feature_barcoding version default to 0.11.1.
• In Cellranger_create_reference workflow: upgrade cellranger_version default to 7.1.0.
• In Cellranger_vdj_create_reference workflow: upgrade cellranger_version default to 7.1.0.
• In Spaceranger workflow: upgrade spaceranger_version default to 2.0.1.

2.3.0

• New Features:
  • Add support for Fixed RNA Profiling to Cellranger workflow.
• Updates:
  • In Cellranger workflow:
    • Upgrade cellranger_version default to 7.0.1.
    • Upgrade cellranger_arc_version default to 2.0.2.
  • In Cellranger_create_reference workflow: upgrade cellranger_version default to 7.0.1.
  • In Cellranger_vdj_create_reference workflow: upgrade cellranger_version default to 7.0.1.

2.2.0

• New Features:
  • Add Nanostring GeoMx DSP workflows. It consists of two steps:
    • GeoMx_fastq_to_dcc workflow to convert FASTQ files into DCC files by wrapping Nanostring GeoMx Digital Spatial NGS Pipeline.
    • GeoMx_dcc_to_count_matrix workflow to generate probe count matrix from DCC files with pathologists’ annotation.
• Updates:
  • Spaceranger workflow:
    • Add support on 10x Space Ranger v2.0.0.
    • Add human_probe_v2 Probe Set for FFPE samples, which is compatible with CytAssist FFPE samples.
  • Upgrade cumulus_feature_barcoding_version default to v0.11.0 for Feature Barcoding in Cellranger workflow.
• API Changes:
  • Across all workflows, for AWS backend:
    • All workflows now have awsQueueArn input, which is used for explicitly specifying the Arn string of an AWS Compute Environment.
    • Remove awsMaxRetries input for all workflows. Namely, use Cromwell’s default value 0.
• Bug Fix:
  • Fix the issue on localizing GCP folders in Cellranger workflow for ATAC-Seq and 10x Multiome data.