chore(main): release 1.2.0

[ftabaro]

🤖 I have created a release beep boop

1.2.0 (2024-05-16)

Features

• add rulegraph (804bb1c)
• add workflow documentation.md (3fb9713)
• allow to download only RMSK annotation only for selected chromosomes (92abc0a)
• bump Docker environment version (f899fd3)
• init implementation of unit tests - currently not all work (d9eb2e3)
• port to Snakemake 8 (9a0a8af)
• refactor common functions. Now pipeline requires sample sheet to work (d723b12)
• rename and cleanup integration tests folder to comply with WorkflowHub folder tree (2e908ca)
• updated Dockerfile (85f4b02)

Bug Fixes

• add resources/sample-sheet.csv and update integration tests config files accordingly (d61b396)
• build_trna_matrix, sort columns according to the sample sheet order (e97ee2e)
• clean .gitattributes (8637d9c)
• clean deseq2 rules (bc33426)
• cleanup Snakefile (8c0f6df)
• coverage_tRNA now makes tmp folder in the correct folder (9b22e04)
• fix fastqc_markdup input function and command (919d088)
• fix logging in download RMSK script (dcf7f29)
• make filename regex more general (01eb56f)
• port all rules to new functions (8488e66)
• protected file path as strings, remove comments (157d98e)
• remove commented line (57761e1)
• remove shadow directive. As of Snakemake 8.10.0 this is not working in conjunction with Apptainer and Slurm (602b112)
• remove unneeded files (2afaea4)
• SalmonTE, polish shell code (13e16eb)
• sorting of tRNA count matrix columns (ac1e1e4)
• SSL error on some platforms (198cbd0)
• STAR, properly handle log files (ba0c2c7)
• STARTE, properly hande log files (fde3c36)
• trim rules now have stats files as logs, removed unparsable log files from output (de2bed0)
• update GH Actions workflow to match new test folder tree, add unit tests (0e2a836)
• update Snakefile to align with new config (efa5b57)
• write lfc-shrinked table to the correct file (e5e3c60)
• YTE template now is a param instead of an input file (2aab702)

---

This PR was generated with Release Please. See documentation.