nf-encyclopedia v1.1.0

[1.1.0] - 2023-04-12

Fixed

• Fixed our conversion from EncyclopeDIA outputs to an MSstats input, which was dropping proteins due to mismatched protein accessions.

nf-encyclopedia v1.0.1

[1.0.1] - 2022-12-14

Fixed

• Fixed issue where the docker image would not build in M1 macs.
• Excel compatibility error due to row names in MSstats ouput.
• Issue where the pipeline would break if non-valid R names are given.
• Fixed and documented an issue where tests would not run locally due to a docker tag.

nf-encyclopedia v1.0.0

[1.0.0] - 2022-10-03

Changed

• Renamed params.ms_file_csv to params.input
• Updated EncyclopeDIA parameters to match GUI defaults.
• Retries should automatically occur when MSconvert hangs
• Renamed EncyclopeDIA processes to be more intuitive.
• The group column in the input file is now optional
• *_postfix parameters were renamed *_suffix.

Added

• Added full support for MSstats

Fixed

• Correctly use -a false when building a chromatogram library.
• MSstats now outputs into the results directory.

nf-encyclopedia v0.5.0

[0.5.0] - 2022-08-26

Changed

• Parameters updated to be more user-friendly.
• Scripts are now in the bin directory, instead of the Docker containers.
• Used logic from nf-core to scale resources on retries.
• Now using the email argument again to get a custom message.
• Removed the use of storeDir

Added

• Reports for pipeline runs.
• Created a public nf-encyclopedia Docker image for everything except msconvert.
• A nearly complete system test using small mzML files.

nf-encyclopedia v0.4.2

[0.4.2] - 2022-07-19

Changed

• Removed email argument in favor of using the default nextflow run -N <email>.
• Removed debug and echo statements from modules.

nf-encyclopedia v0.4.1

[0.4.1] - 2022-07-12

Fixed

• Updated GitHub Actions release workflow.

nf-encyclopedia v0.4.0

[0.4.0] - 2022-07-12

Added

• This changelog!
• Completely reworked pipeline since last release. Note that we were just using the main branch as our release version, but I prefer occasional manual releases for stability.

v0.3

Global runs

v0.2.1

Tag to add store_dir back and test the environment functionality.

v0.2.0

Switch to input file lists and other upgrades