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CHANGELOG.md

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Changelog

1.2.0 (2024-11-12)

Features

  • coverm++ (4b170ac)
  • demand snakemake 8 (5cec580)
  • disable crams in prerpocessing (f329758)
  • disable crams in quantify (c618038)
  • group jobs by sample, update profile (658ae38)
  • import helpers. insert reads into prerpocess. remove per library report (af3f230)
  • insert hosts into preprocess (4c285c0)
  • multqc handles more files (4d44cad)
  • point to base env and clean other (b1b34e0)
  • refactor fastp. use wrappers (da1a88d)
  • refactor quantify (e63eca6)
  • refactor quantify (d59ce09)
  • refactor ribodetector (cee57ef)
  • refactor ribodetector (bc4f921)
  • remove fastp fastqcs from report (9323aec)
  • remove fastp functions (5eda525)
  • separate bowtie2 env from quant (71a54a6)
  • update quantify rule names, fix multiqc output (96cb3e8)

Bug Fixes

Performance Improvements

  • add fastq to group (ee27676)
  • disable group in bowtie2 (e3a26e1)
  • fastp: default extra string (1c9dfc4)
  • profile: increase ram for star index (06bc617)

1.1.2 (2024-10-04)

Bug Fixes

1.1.1 (2024-10-01)

Bug Fixes

  • preprocess/index: make params.prefix str so caching works (2a8a205)

1.1.0 (2024-08-06)

Features

1.0.1 (2024-06-17)

Performance Improvements

  • raise ram for aggregators (258ec0f)

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