optimus_v3.0.0

• Removed the Zarr formatted matrix and metrics outputs and replaced with Loom
• Removed EmptyDrops for sn_rna mode
• Updated the Loom file attribute names: CellID to cell_names, Gene to gene_names, and Accession to ensembl_ids
• Added metrics for mitochondrial reads
• Added an optional input for the BAM basename; this input is listed as ‘bam_output_basename’ and the default is 'sample_id'

smartseq2_v4.0.0

• Added loom output and removed the zarr output

• Loom file attribute names have changed: CellID: cell_names, Gene: gene_names and Accession: ensembl_ids

• Loom file name has changed from out.loom to "sample_id".loom

• Added expected counts in addition to the TPMs in the loom matrix

MultiSampleSmartSeq2_v2.0.0

• Removed zarr formatted matrix SS2 multi-samples.
• Removed the boolean option to create loom file as default.
• Renamed the loom file name to plateid
• Added zarr file like global attributes to the loom file.
• Merged all loom file creation script into one Dockerfile and removed the individual docker images.

optimus_v2.0.0

optimus_v2.0.0 release change-log:

• Fixed a bug that resulted in emptyDrops output being incorrect
• Updated workflow to WDL 1.0

MultiSampleSmartSeq2_v1.0.0

MultiSampleSmartSeq2_v1.0.0 release change-log:

Initial pipeline release

smartseq2_v3.0.0

Smartseq2_v3.0.0 release change-log:

• Added single end support for the Smart-seq2 Single Sample pipeline
• Removed a previous version of a standalone single-end pipeline

optimus_v1.4.0

Optimus 1.4.0 release change-log:

• Addition of support for V3 chemistry
• Addition of input parameter validation step
• Greatly improved documentation
• Updates to Zarr outputs:
  • Addition of a zarr schema version tag (this is v1.0.0)
  • Updated Zarr schema (see documentation)
  • Header lengths bug fix: headers are no longer being truncated

smartseq2_v2.5.0

• Remove max_retries parameter so that a default value can be set by the workflow options

optimus_v1.3.6

This release adds the following features:

• EmptyDrops output is now included in the ZARR output
• The GTF modification step is removed from the scatter, resulting in better performance and caching
• Memory of several tasks is increased
• The ZARR output is now compulsory and the relevant input flag has been removed
• Support for loom format has been added and an new optional flag dictates if the file is created
• Documentation has been updated

optimus_v1.3.3

• Release a new patch version of Optimus with an ambitious memory allocation for CalculateCellMetrics task.
• This version and all future versions have been scientifically validated on Mouse reference version mm10 (GRCm39, Gencode M21).