v1.0.0

1.0.0 (2024-06-14)

⚠ BREAKING CHANGES

• release 1.0.0

Features

• add gha updater (6dd2b43)
• add per gene counts with featureCount (3f8fd05)
• bowtie2: write index within the rule (f171f0c)
• bowtie2: write index within the rule (5f17b3f)
• compress all count data (72e9a9e)
• compute counts over genes (a222296)
• coverm: coverm + cram (dbe1b09)
• coverm: coverm + cram (869df57)
• coverm: delete dead code. -F 4 (0661d62)
• coverm: delete dead code. -F 4 (dea6a0a)
• fastp: remove process substitution and use level 9 compression (7a685dd)
• fastp: remove process substitution and use level 9 compression (a45a22f)
• fastp: remove process substitution and use level 9 compression (6834cc5)
• fastp: use process substituttion and pigz -11 (9b956cb)
• fastp: use process substituttion and pigz -11 (4f3b0b9)
• fastp: use process substituttion and pigz -11 (c49b538)
• features: add the usual suspects (a2ec8c4)
• features: move databases and mag catalogue. @ in mag mock (f9c5f54)
• get gene quantifications with htseq (1a461e0)
• ignore rstudio stuff (651d20e)
• ignore rstudio stuff (39767ac)
• params: add @ as the default mag-contig separator (e33b82d)
• params: add common coverm params (47f0caf)
• params: add common coverm params (7a00763)
• pre-commit: add conventional-pre-commit (b6df867)
• pre-commit: add R linters (b31ddec)
• pre-commit: autoupgrade (99ec679)
• pre-commit: autoupgrade (e156263)
• pre-commit: update all hooks (e7cf184)
• preprocess: set adaptors in samples. refactor. Update readme (649d019)
• quantify: refactor (be70cab)
• quantify: refactor coverm functions (6a33bc0)
• README: update repo name (d516776)
• README: update repo name (c62c2be)
• reads: refactor file and adaptor functions (ba42fec)
• reads: split into subworkflows (d6bc3ba)
• reads: split into subworkflows (1616a6f)
• report: add the definitive report rule (a708af3)
• report: raise ram (f1aaf9d)
• report: raise ram (ae130be)
• ribodetector: remove temp (86c5ac2)
• ribodetector: remove temp (0617fd3)
• star: compress within the rule, raise compression level (eca2288)
• star: compress within the rule, raise compression level (d93087b)
• star: refactor functions (6258c9b)
• star: refactor functions (85b0467)
• the big rename (0d9833f)
• update github actions (2e9d284)
• Update readme (11d0942)
• Update readme (19c9962)
• Update readme (a6e5095)

Bug Fixes

• add prefixes to htseq and subread outputs to prevent a prefix loop (974402a)
• add user and permissions to rsync (b52d0fd)
• folder: consistent folder names (89603a6)
• folder: consistent folder names (22f9066)
• folder: consistent folder names (15ba09b)
• folder: consistent folder names (446d25b)
• gha: add temporary snakemake-action (78945ad)
• kraken2: use for loop over mapfile (7a6afbf)
• kraken2: use for loop over mapfile (25faa7b)
• point to the correct branch in the badge (aa9c2b6)
• pre-commit: update hooks (b04c596)
• remove unused code (8f1b473)
• report: raise preprocess report ram (80c84bc)
• report: raise preprocess report ram (4a7f1b7)
• report: rename rules (0a2197b)

Miscellaneous Chores

• release 1.0.0 (0a18829)