v1.4.0

1.4.0 (2024-12-04)

Features

• add slurm, cache, test scripts (4ab571f)
• bracken (8183326)
• cache rule (e7ac7bd)
• configfile (ebac6c0)
• do bracken on all taxonomic levels, only show species in multiqc (d8efee3)
• get the aggregated counts directly from subread (7f8900e)
• use col1 and col2 to see if it reduces ram usage (2f527c2)
• use subread from wrappers (e9971d8)

Bug Fixes

• add all the bracken files to the copy in /dev/shm (c4df691)
• dont use slurm within slurm , dumbass (acf4c57)
• get the correct featurecounts file (a2beada)
• handle manually subread sample renaming; corner case in csvtk (0a15ae8)
• put clean in the preprocess group (24be3b8)
• put fastq in the correct group (e6a3462)
• put slurm executor (f4b65f6)
• put tmp folders for index and map (a3c11ab)
• remove more mentions to coverm (900e667)
• remove tmp dirs if they exist (ccf4e09)
• rerun incomplete (99941d1)
• undo bracken copy (47f72eb)
• use proper featurecounts file (d76c680)

Performance Improvements

• cache but omit software versions (09eb311)
• disable groups (6d17ce8)
• double ram on subread join (f3c356f)
• put reads in a group and disable localrule (e7c2ad7)
• raise ram to tsv join (a06dcad)
• subread: raise ram to 4GB (b0ea99a)

v1.3.0

1.3.0 (2024-11-29)

Features

• coverm: mark individual files as temporary (25e4c86)
• coverm: rearrange files again (8058735)
• coverm: remove functions (015c4f8)
• htseq: do not compress output and make it temp (6d9159c)
• remove r packages, update and pin environments (5785f85)
• restructure bowtie and use csvtk to join files (acc9ddf)
• subread: introduce middle step (365d41e)
• subread: quantify trnas and rrnas too (d459a74)
• subread: solve dependency; add reports to multiqc (2b7b9a3)
• substitute custom r script for csvtk (0cacb96)

Bug Fixes

• bowtie2: small index (7f17e44)
• give multiqc the correct files (1f35182)
• htseq: remove mention to file (53465d9)
• remodel to take the gff from dram (7a5d362)

v1.2.0

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

• fastp: correct group name (2751414)
• remove mention to ram (e009781)
• star: point to u1, u2 (f6344f1)
• star: point to u1, u2 .fq (fb68d67)

Performance Improvements

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

v1.1.2

1.1.2 (2024-10-04)

Bug Fixes

• decompress mag gtf (db32655)

v1.1.1

1.1.1 (2024-10-01)

Bug Fixes

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

v1.1.0

1.1.0 (2024-08-06)

Features

• pin dependencies (1d39136)

v1.0.1

1.0.1 (2024-06-17)

Performance Improvements

• raise ram for aggregators (258ec0f)

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)

v0.0.1

Merge pull request #9 from 3d-omics/reform

feat: Reform

v0.0.0.9000

Update README.md