History

0.3.6 (2018-10-05)

• Bumped Snakemake version to deal with permission problems when using the script directive.

0.3.5 (2018-05-29)

• Added the option to execute jobs in a singularity container
• Added lts-workflows-sm-scrnaseq-slim Conda package, which is only the workflow without the tools. To be used with “–use-singularity”
• Modified Docker images to install to “base” environment rather than to “snakemake”

0.3.4 (2018-05-25)

• Added the option to group sets of cells and run as group jobs
• Changed to use scater v1.6 and SingleCellExperiment
• Changed to use “runtime” as a rule resource rather than a parameter

0.3.3 (2018-05-07)

• Rewrote QC report from scratch
• Added filtering of contaminating cells based on marker gene expression
• Changed QC config structure
• No longer built for Python 3.5 (dumping settings to yaml relies on that dicts are ordered, which was implemented in 3.6)

0.3.2 (2018-04-23)

• Rewrote QC report to fit better as part of a workflow
• Added biotypes to the QC and filtering steps
• Removed unnecessary logs to reduce the number of files created
• Explicitly include all files generated by the workflow rules
• Flag more files as temporary to reduce space usage
• General clean up of the code

0.3.1 (2018-04-17)

• Changed to use R-markdown 1.8 due to error in the conda-forge recipe for 1.5.

0.3.0 (2018-04-09)

• Added QC and filtering
• Changed CI and testing Docker images

0.2.0 (2017-01-30)

• Simplify test setup
• Make pytest-ngsfixtures optional
• Use picard instead of samtools rules for sorting
• Update rseqc rule for empty fastq input (#37)
• Add multiqc rule (#33)
• Add rule for rpkm/count matrix (#31)
• Add gene entry to gtf file (#28)

0.1.0 (2017-02-12)

• First release on conda.