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: v0.3.1...v0.3.2

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: v0.3.0...v0.3.1

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: v0.2.7...v0.3.0

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: v0.2.6...v0.2.7

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: v0.2.5...v0.2.6

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: v0.2.4...v0.2.5

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: v0.2.3...v0.2.4

scpca-nf v0.2.3

What's Changed

• Increase maximum retry attempts from 2x to 3x

Full Changelog: v0.2.0...v0.2.3

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: v0.2.0...v0.2.2

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: v0.2.0...v0.2.1