V1.14

What's Changed

• updates phippery version in Dockerfile where public image is generated from, in order to patch this phippery bug
• added dockerfile, updated config to point to new container by @jgallowa07 in #79

New Contributors

• @afonsoguerra made their first contribution in #73

Full Changelog: V1.13...V1.14

Add outputs to the aggregate organisms module

What's Changed

• Add outputs to the aggregate organisms module by @sminot in #75

Full Changelog: V1.12...V1.13

Patch Virscan Workflow

This version patches two things in the Virscan workflow as brought up in issue #68. The changes can be summarized by those in #69.

Change defaults and gzip output csvs

Make output of wide csv's the default, and gzip them.

Update phippery container version

Small release which simply updates the version of phippery in the config to 1.2.0

Added BEER workflows

This version adds

• the default edgeR workflow
• the optional BEER workflow.

It also updates the test files to include a smaller test set for BEER.

Add results columns for max_ebs_hits and mean_ebs_hits

In the output file aggregated_data/organism.summary.csv.gz, add columns:

• max_ebs_hits
• mean_ebs_hits

Those metrics will report the values for just the subset of organisms which satisfy the threshold for a hit (excluding discordant results).

V1.07 - Explicitly define variable types for peptide / organism outputs

Bugfix: Ensure that 'hit' column from the peptide EBS table is interpreted as a string for all datasets.

V1.06

Bugfix - percent_peptides_between_10_and_100 was not being calculated correctly in the sample annotation table.

V1.05

Update the behavior of aggregate_by_organisms to filter overlapping peptides by exact sequence matching.

Users no longer need to specify a gene name and position when aggregating results by organism.