optimus_v1.3.2

Update Optimus patch version (#241)

snap-atac_v1.0.0

Initial release of the snap-atac pipeline. The pipeline can process single-cell ATAC-seq fastq files that have been pre-tagged with cellular barcodes and produce an output snap file that includes peak summarization.

optimus_v1.3.1

This release includes fixes to the Optimus gene id outputs.

optimus_v1.3.0

This release is a backwards incompatible change for the Optimus pipeline. The output matrices now contain gencode v27 gene ids in addition to gene names to comply with outputs from other pipelines and expectations of downstream services.

optimus_v1.0.0

• The first major version release for the Optimus pipeline.

v0.3.0

• Reorganized skylab repository

v0.2.1

Fix to Smart-seq2 workflow to avoid file name conflicts. The Smart-seq2 workflow has two sub workflows, and some of the files, such as bam files, were named identically in both sub workflows in v0.2.0. (Having unique names is important when copying all the outputs to a single directory, which occurs when making submissions to the HCA ingest service, among other things.)

10x has not changed in this version.

v0.2.0

A new version of the Smart-seq2 pipeline that uses HISAT2 for alignment (it previously used STAR). For more details on the updated pipeline, see the wiki. The 10x pipeline remains unchanged.

v0.1.0

This initial release marks progress on a 10x and a SmartSeq2 control pipeline, and a MVP of a new 3' pipeline. It sets a starting point so that we can increment on a new SmartSeq2 pipeline.