diff --git a/CHANGELOG.md b/CHANGELOG.md index 367ca42..0d7bb34 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,5 +1,37 @@ # GRAPE-nf Changelog +## Version 1.0.0 + +First IHEC release + +- Whole pipeline refactoring - #51 +- Fix wrong merging information - #55 +- Add ability to use regex for reference prefix in `bigwig` step - #17 + +Additional improvements and fixes: + +- Use 2/3 of the process memory in `mapping` +- Increase `quantification` memory in IHEC resources config file +- Update `sambamba` version to `0.7.1` +- Update `bamstats` version to `0.3.4` +- Enable autoMounts for Singularity by default +- Add script to prepare input `FASTQ` files from `BAM` files +- Fix issue in field order when reading input `BAMs` +- Add `gtf` and `gff` to supported file types in CI script +- Sort transcriptome `BAMs` before merge +- Remove `test.sh`, update CI tests and TravisCI configuration file +- Fix workflow for input `BAMs` and add test profile +- Add threshold option to infer experiment script and add corresponding pipeline parameter +- Fix read group attributes in `mapping` + +IHEC specific changes: + +- Move all IHEC documentation to `ihec-setup.md`, update and clean up +- Clean up pipeline config and use single IHEC image for the IHEC profile +- Add script to pre-fetch the IHEC Singularity image +- Add the IHEC profile to TravisCI config +- Update test data and checksum, add checksums for the IHEC profile + ## Version 0.4.1 - Fix wrong comment in config file braking pipeline execution