v1.6.0

1.6.0 (2025-05-13)

Features

• update multiqc so it shows filenames instead of samples (32da448)

Bug Fixes

• cache mags and index (78ab60b)
• put quantify bam files with mag.sample.lib.bam format (0c1c478)
• there is no default profile now (ca7156b)

v1.5.0

1.5.0 (2024-12-02)

Features

• use config.yml (586d5c9)

Bug Fixes

• place coverm files so mag catalogue stays outside the sample name (f540560)

v1.4.0

1.4.0 (2024-11-26)

Features

• populate profiles (79244a7)

Bug Fixes

• pick everything from devel (7e98394)

v1.3.0

1.3.0 (2024-10-22)

Features

• compress coverm files (b4cd436)
• cover, mags, multiqc; delete useless code; compress coverm files" (af82953)
• insert mg_preprocess and delete redundant code (b1532a3)
• pin dependencies (711e700)
• rename rules and add meta-rule (ab9e99f)
• simplify coverm file names, remove singlem script (a660727)
• use helpers and preprocess modules. update params (89915b4)

Bug Fixes

• add idxstats, ask for folder as output too (de73fd3)
• typo (50799a5)

v1.2.0

1.2.0 (2024-09-02)

Features

• start adding support for nonpareil multiqc reports (047a216)
• update nonpareil and multiqc so they do the jsoning and the reporting (5fc6bdd)

Bug Fixes

• add missing script (39fbc23)
• disable process substitution in fastp since multiqc can't handle it properly (f593508)
• remove group from import (6071514)
• wrong path (e7ecb4e)

v1.1.2

1.1.2 (2024-08-08)

Bug Fixes

• update multiqc so it properly reports fastp (ca1fbb2)

v1.1.1

1.1.1 (2024-08-07)

Performance Improvements

• correct kraken2 rule name in profiles (870167c)

v1.1.0

1.1.0 (2024-08-06)

Features

• pin dependencies (2f53db9)

Bug Fixes

• add cache rule to the bottom (2c3c9fd)
• nonpareil (3ac7cc3)
• singlem: pin smafa version (ef89c21)

v1.0.1

1.0.1 (2024-06-06)

Bug Fixes

• fix rule names in profile (79ca5a0)

v1.0.0

1.0.0 (2024-05-13)

Features

• 0 threads when copying, rename group (83b4290)
• accelerate fastp (e5ba830)
• adaptors: adaptors should be explicitely written (cc12e74)
• add execution groups (2d21e86)
• add fastp to preprocess group (df0df2e)
• add groups in run_slurm (778f2a4)
• add indexes and references to cache (16cc736)
• add micro profile (6aad3bf)
• add profile (7e0fc8a)
• Add run_slurm [skip ci] (a3123b1)
• bowtie2: disable minimizer compression (dd66c46)
• bowtie2: get ram from params (9c8162d)
• bowtie2: increase compression level (d870e95)
• bowtie2: remove bottleneck (933bece)
• cache bowtie2 indexes (4ec4a55)
• cache omitting software versions (f91122c)
• clean code (2006df1)
• consistent naming (cb49e19)
• correct column names in samples.tsv (016f850)
• coverm: accept cram as input (26b601b)
• coverm: refactor aggregator function (74dcd06)
• cram to fastq in quantify. add defaults to profiles (4055a4c)
• delete all the code mentioning SE reads (57f3ac3)
• extract threads and resources to profile in preprocess (c854f80)
• extract threads and resources to profile in quantify (5846fc6)
• extract threads and resources to profile in reference/recompress (0292ca0)
• extract threads and resources to profile in report (a46a0b5)
• extract threads and resources to profile in samtools (d5653ff)
• fastp: insert extra trims to fastp (71dee60)
• fastp: manage more elegantly the adaptors and the NAs (0a81ad8)
• fastp: put an assert just in case (c3fc4a9)
• fastp: refactor functions (854d1e3)
• fastp: remove temps, raise compression level (afe88aa)
• final profiles (ca3cde5)
• folders: consistent reordering (3358c0a)
• functions: remove unused code (4a3acfa)
• gha: split into steps (269ec70)
• gha: upload logs as artifacts on failure (b52692a)
• handle big and small bowtie2 indexes (af2f956)
• humanize default profile (5a4c615)
• in bowtie2 map rules, clean past tmp bam files (8a68596)
• join heavy processes into a single group (e52712a)
• kraken2 as a service (ed02c97)
• kraken2 as in mg_assembly (201af9b)
• kraken2: print the hostname (a91735f)
• lower compression level, don't produce unpaired (60e2c67)
• mark singlem fastqs as temp (62c3943)
• mem_mb -> mem_gb (58d085f)
• nonpareil: cleaner code (345f381)
• organization: dunder all the important files (0c6b088)
• params: remove mentions to extra fields (f489d2f)
• pre-commit: add R linters (df017d8)
• pre-commit: add R linters (cd26577)
• pre-commit: raise message to the top (aa6b764)
• preprocess: run everything by default, and everything but singlem on testing (5c949c2)
• raise threads for bowtie (67ca596)
• raise threads for bowtie (8d02fd0)
• readme: Update badges (d5a4e1d)
• readme: update with new control files (670c818)
• reads: refactor functions (b8952ac)
• reads: split into subworkflows (e05481d)
• remove commented code. remove tmp of links (4bc96c1)
• remove dead code. cache correct files (b1eaa94)
• remove old scripts (87bb8e0)
• rename and relink preprocessing (3d73aef)
• rename and relink reads (d44c60c)
• rename and relink reference (c579973)
• rename and relink report (2e7dbbf)
• rename and relink stats (b206ee6)
• rename helpers (374a63e)
• rename rules and add fai to cache (486a57f)
• rename rules, create bowtie2 indexes in their place, and with multiext (9935c4b)
• reorganization: env.yml => environment.yml (cb685d3)
• reorganize config/params.yml ([da9af8e](https://github.com/3d-omics/mg_quant/commit/...