chore(main): release 1.0.1

[ftabaro]

🤖 I have created a release beep boop

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)

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[ftabaro]

🤖 Release is at https://github.com/boulardlab/3t-seq/releases/tag/v1.0.1 🌻