v1.1.0

1.1.0 (2024-03-12)

Features

• containerize pipeline's output (a3b4086)
• enable caching for all references and STAR indexes (bc99687)
• test Snakemake report generation (c2c0f46)
• update Dockerfile (bb47f34)

Bug Fixes

• add singularity-args and reformat lines in CI (598de8d)
• cleanup Snakemake test profile (2c2cdf7)
• formatting edit_condition_file.py (e26f101)
• properly download using UCSC API. Fix all paths and enable caching (db8da50)
• switch to wget and write some logging when downloading genome annotations (c49e4ff)

v1.0.1

1.0.1 (2024-03-06)

Features

• add example Slurm configuration (96ce038)
• decouple TE, tRNA and single copy genes pipelines. Allow users to decide which branches to run.#3 (d3b12e4)
• describe how to run tests (46e023f)
• DESeq2 reference is now separate for each sequencing library (b4cf102)

Bug Fixes

• allow deseq2 ananlysi with different variables and different levels (76c2562)
• fix deseq2 scripts to look for correct column names (ffc4537)
• fix problem with SalmonTE quant input array on single-end libraries (3fd51ff)
• fix Snakemake version to be below 8 (5fa9be3)
• look for correct column name in edit_conditions_file.py (e60456e)
• make test dataset smaller to let it run in GH Actions (17ac70d)
• pin all conda packages versions (feddd48)
• remove params.mem_mb from starTE rules (b6f1848)
• restore test profile (c50b75e)
• revert alpine base for SalmonTE Docker (bfb4a48)
• switch to miniconda3-alpine as base (7ac38c7)
• test config now has library-specific deseq2 reference level (44d4b43)
• typo (6e64c84)
• update docs (c811991)

Miscellaneous Chores

• release 1.0.1 (25c11bc)

v1.0.0

1.0.0 (2023-11-17)

Features

• add file for Snakemake workflow catalog (cf8723d)
• add pseudocounts to count matrix if cannot estimate size factors (219d665)
• explicit all star outputs (2f2d7b9)
• start basic documentation (1d57ff5)
• update Dockerfile (877bf88)

Bug Fixes

• add tests (418381b)
• add text data (328781a)
• config directory (bbf4926)
• correctly pass genome label to get_rmsk.py (8157a11)
• edit_condition_file rule (adb0a5e)
• mkdir (646a3d4)
• mv configuration docs to specific README file (a8adec4)
• pin R version for SalmonTE (b7c238b)
• polish (5d4b3b7)
• remove useless print (fa11e58)
• snakemake variable (a123c63)
• syntax (1d20176)
• update TOKEN in main CI workflow (3d9faaa)