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CHANGELOG
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#### 1.4.0 2024.08.16
* Add GitHub Actions automation
#### 1.3.8 2024.08.12
* Misc bugfixes
#### 1.3.7 2024.07.29
* Misc bugfixes
#### 1.3.6 2024.07.10
* Force samtools split to open required no. of files, use default params instead of dummy files.
* Mitigate wiz alert for batch job definition in drugseq aws account, fix environment in notification email.
#### 1.3.5 2024.07.03
* Refactors pipeline to adopt community best practices for pipeline organization and parameters validation
* Outputs a new file mrk_dependent_software_versions.yml with the versions of all tools and packages used
* Refactors downsampling logic to improve clarity, flexibility, and speed
* Various bugfixes
#### 1.3.4 2024.06.20
* Fix bug where wells are downsampled to nearly 0
#### 1.3.3 2024.06.11
* replace exact downsampling with probabilistic
#### 1.3.2 2024.06.06
* Fix crash with bad data type inference for violin
* Propagate user email parameter to GED
* Fix Too many indexers error
#### 1.3.1 2024.05.21
* Add functionality to downsample wells that have too many reads prior to alignment
* Update DRAGoNreport and STARsoloReport files with more descriptive headers and additional statistics
* Correct inaccurate % loss statistics in DRAGoNreport, STARsoloReport
#### 1.3.0 2024.05.16
* Produce plate_heatmap.png output file
* Add REQUIRED parameter --ISID for use with the AWS profile
* Various bugfixes
#### 1.2.4 2024.04.03
* Hard fail pipeline on data quality issues when `--Demux.data_quality_errors = raise`
#### 1.2.3 2024.03.26
* Add demux.json `plate_map` field for diagnostic purposes.
#### 1.2.2 2024.02.09
* `--workflowMode single` is deprecated
* Improve readout from demultiplexed counts QC report
#### 1.2.1 2023.12.06
* Increase threshold for "excessive read counts"
#### 1.2.0 2023.11.01
* Add data quality checkpoint
#### 1.1.3 2023.08.17
* Catch up on manual change log
* Add TPM and FPKM output
* Onboard KSeq++, BAMtools, Eigen3 instead of custom adaptors
* Delete zstr
* Correct Rescue formula
* Use standard C++23
* Handle more cases of malformed metadata
#### 1.1.2 2023.02.23
* Implement unit tests
* Rework mix-and-match profile configurations
* Remove dead code
* Checkout zstr as a submodule
* Add Jenkins job to execute unit tests
#### 1.1.1
* Port processes Demultiplex, SplitBAM, and Deduplicate to C++
* Remove BED output
#### 1.1.0
* Strengthen duplicate detection using updated criteria
* Conditionally swap order of STAR and SplitBAM processes based on whether two-pass mode is requested
* Augmented reporting of UMIs in the BED file
* Subject noBC reads to featureCounts and CollapseMultimappers
* Support launching from the stash bitbucket server
* Fix EM multimapper resolution strategy
* Minor fixes and tweaks
#### 1.0.0
* Added BED output for UMI-level introspection
* Spawn only a single STAR job instead of --Demux.split
* Add descriptive tags to processes for ease of tracking when running in background
* Remove --IO.tmpdir
* Changed default for --Demux.mismatch to 1
* Added check for unique well names
* Barcode distance check now tests for up to 2 * Demux.mismatch, and errors if observed. Resolves issue processing PID22680.
#### 1.0.0rc3
* Accepts BCL as input
* Simplified --IO.R1, --IO.R2 to --IO.fastqdir, --IO.sampleName
* Various bugfixes
* Restored support for nextflow version 21.04.3 Renamed DRAGoN{/main=>}.nf, STARsolo{/main=>}.nf. Moved accessory scripts to common bin/.
#### 1.0.0rc2
* Added additional barcode sanity checks to Preprocessing.Demultiplex
* Merge intermediate BAM files at the end, for downstream debugging
* Various bugfixes
#### 1.0.0rc1
* `scripts/parse_metadata.py` properly handles metadata files with unallocated wells.
* Separated the STARsolo and DRAGoN workflows. Removed top-level main.nf. THIS IS A BREAKING CHANGE!
* Changed --Dedup.ambiguous [None->Unique]. THIS IS A BREAKING CHANGE!
* Refactored to utilize moduleBinaries feature from nextflow 22.10 to allow standalone execution of python scripts. Minimum required version of nextflow is therefore 22.10. THIS IS A BREAKING CHANGE!
* Updated awsbatch profiles
* Renamed profiles. merck_ctc -> ctc_hpc_sge, merck_aws -> {ctc_hpc_awsbatch,ssngsi_awsbatch_06_1q}. THIS IS A BREAKING CHANGE!
* If --IO.star directory doesn't exist or is empty, builds genome indices on-the-fly (requires --IO.fasta and --IO.gtf).
#### 1.0.0b2
* Removed scripts for running legacy pipelines
* Added `scripts/parse_metadata.py` to simplify the creation of `barcodes.txt`, `params.yml`, and the output directory.
* Multimapped reads tracker now holds its memory across chromosomes within a barcode, allowing for greater accuracy when using a multimap handler.
* Uniform and PropUnique handlers tested and verified.
* User may now select multiple multimap handlers for the same run of both STARsolo and DRAGoN. The "None" handler will always be selected.
* Renamed workflow script from `STARsolo.nf` to `main.nf`.
#### 1.0.0b1
* Initial implementation of DRAGoN, together with STARsolo, as a nextflow pipeline.