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.

2.1.1

Make cumulus WDL workflow work with Cromwell v81+. (PR #348 )