# nf-core/mag: Changelog

The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).

## v2.3.1 - [2023-06-19]

### `Fixed`

- [#458](https://github.com/nf-core/mag/pull/458) - Correct the major issue in ancient DNA workflow of binning refinement being performed on uncorrected contigs instead of aDNA consensus recalled contigs (issue [#449](https://github.com/nf-core/mag/issues/449))
- [#451](https://github.com/nf-core/mag/pull/451) - Fix results file overwriting in Ancient DNA workflow (reported by @alexhbnr, fix by @jfy133, and integrated by @maxibor in [#458](https://github.com/nf-core/mag/pull/458) )

## v2.3.0 - [2023/03/02]

### `Added`

- [#350](https://github.com/nf-core/mag/pull/350) - Adds support for CheckM as alternative bin completeness and QC tool (added by @jfy133 and @skrakau)
- [#353](https://github.com/nf-core/mag/pull/353) - Added the busco_clean parameter to optionally clean each BUSCO directory after a successful (by @prototaxites)
- [#361](https://github.com/nf-core/mag/pull/361) - Added the skip_clipping parameter to skip read preprocessing with fastp or adapterremoval. Running the pipeline with skip_clipping, keep_phix and without specifying a host genome or fasta file skips the FASTQC_TRIMMED process (by @prototaxites)
- [#365](https://github.com/nf-core/mag/pull/365) - Added CONCOCT as an additional (optional) binning tool (by @jfy133)
- [#366](https://github.com/nf-core/mag/pull/366) - Added CAT_SUMMARISE process and cat_official_taxonomy parameter (by @prototaxites)
- [#372](https://github.com/nf-core/mag/pull/372) - Allow CAT_DB to take an extracted database as well as a tar.gz file (by @prototaxites).
- [#380](https://github.com/nf-core/mag/pull/380) - Added support for saving processed reads (clipped, host removed etc.) to results directory (by @jfy133)
- [#394](https://github.com/nf-core/mag/pull/394) - Added GUNC for additional chimeric bin/contamination QC (added by @jfy133)

### `Changed`

- [#340](https://github.com/nf-core/mag/pull/340),[#368](https://github.com/nf-core/mag/pull/368),[#373](https://github.com/nf-core/mag/pull/373) - Update to nf-core 2.7.2 `TEMPLATE` (by @jfy133, @d4straub, @skrakau)
- [#373](https://github.com/nf-core/mag/pull/373) - Removed parameter `--enable_conda`. Updated local modules to new conda syntax and updated nf-core modules (by @skrakau)
- [#385](https://github.com/nf-core/mag/pull/385) - CAT also now runs on unbinned contigs as well as binned contigs (added by @jfy133)
- [#399](https://github.com/nf-core/mag/pull/399/files) - Removed undocumented BUSCO_PLOT process (previously generated `*.busco_figure.png` plots unsuitable for metagenomics) (by @skrakau).

### `Fixed`

- [#345](https://github.com/nf-core/mag/pull/345) - Bowtie2 mode changed to global alignment for ancient DNA mode (`--very-sensitive` mode) to prevent soft clipping at the end of reads when running in local mode. (by @maxibor)
- [#349](https://github.com/nf-core/mag/pull/349) - Add a warning that pipeline will reset minimum contig size to 1500 specifically MetaBAT2 process, if a user supplies below this threshold. (by @jfy133)
- [#352](https://github.com/nf-core/mag/pull/352) - Escape the case in the BUSCO module that BUSCO can just detect a root lineage but is not able to find any marker genes (by @alexhbnr)
- [#355](https://github.com/nf-core/mag/pull/355) - Include error code 21 for retrying with higher memory for SPAdes and hybridSPAdes (by @mglubber)

### `Dependencies`

| Tool      | Previous version | New version |
| --------- | ---------------- | ----------- |
| BUSCO     | 5.1.0            | 5.4.3       |
| BCFtools  | 1.14             | 1.16        |
| Freebayes | 1.3.5            | 1.3.6       |
| SAMtools  | 1.15             | 1.16.1      |

## v2.2.1 - 2022/08/25

### `Added`

### `Changed`

### `Fixed`

- [#328](https://github.com/nf-core/mag/pull/328) - Fix too many symbolic links issue in local convert_depths module (reported by @ChristophKnapp and fixed by @apeltzer, @jfy133)
- [#329](https://github.com/nf-core/mag/pull/329) - Each sample now gets it's own result directory for PyDamage analysis and filter (reported and fixed by @maxibor)

### `Dependencies`

## v2.2.0 - 2022/06/14

### `Added`

- [#263](https://github.com/nf-core/mag/pull/263) - Restructure binning subworkflow in preparation for aDNA workflow and extended binning
- [#247](https://github.com/nf-core/mag/pull/247) - Add ancient DNA subworkflow
- [#263](https://github.com/nf-core/mag/pull/263) - Add MaxBin2 as second contig binning tool
- [#285](https://github.com/nf-core/mag/pull/285) - Add AdapterRemoval2 as an alternative read trimmer
- [#291](https://github.com/nf-core/mag/pull/291) - Add DAS Tool for bin refinement
- [#319](https://github.com/nf-core/mag/pull/319) - Activate pipeline-specific institutional nf-core/configs

### `Changed`

- [#269](https://github.com/nf-core/mag/pull/269),[#283](https://github.com/nf-core/mag/pull/283),[#289](https://github.com/nf-core/mag/pull/289),[#302](https://github.com/nf-core/mag/pull/302) - Update to nf-core 2.4 `TEMPLATE`
- [#286](https://github.com/nf-core/mag/pull/286) - Cite our publication instead of the preprint
- [#291](https://github.com/nf-core/mag/pull/291), [#299](https://github.com/nf-core/mag/pull/299) - Add extra results folder `GenomeBinning/depths/contigs` for `[assembler]-[sample/group]-depth.txt.gz`, and `GenomeBinning/depths/bins` for `bin_depths_summary.tsv` and `[assembler]-[binner]-[sample/group]-binDepths.heatmap.png`
- [#315](https://github.com/nf-core/mag/pull/315) - Replace base container for standard shell tools to fix problems with running on Google Cloud

### `Fixed`

- [#290](https://github.com/nf-core/mag/pull/290) - Fix caching of binning input
- [#305](https://github.com/nf-core/mag/pull/305) - Add missing Bowtie2 version for process `BOWTIE2_PHIX_REMOVAL_ALIGN` to `software_versions.yml`
- [#307](https://github.com/nf-core/mag/pull/307) - Fix retrieval of GTDB-Tk version (note about newer version caused error in `CUSTOM_DUMPSOFTWAREVERSIONS`)
- [#309](https://github.com/nf-core/mag/pull/309) - Fix publishing of BUSCO `busco_downloads/` folder, i.e. publish only when `--save_busco_reference` is specified
- [#321](https://github.com/nf-core/mag/pull/321) - Fix parameter processing in `BOWTIE2_REMOVAL_ALIGN` (which was erroneously for `BOWTIE2_PHIX_REMOVAL_ALIGN`)

### `Dependencies`

| Tool    | Previous version | New version |
| ------- | ---------------- | ----------- |
| fastp   | 0.20.1           | 0.23.2      |
| MultiQC | 1.11             | 1.12        |

## v2.1.1 - 2021/11/25

### `Added`

- [#240](https://github.com/nf-core/mag/pull/240) - Add prodigal to predict protein-coding genes for assemblies.
- [#241](https://github.com/nf-core/mag/pull/241) - Add parameter `--skip_prodigal`.
- [#244](https://github.com/nf-core/mag/pull/244) - Add pipeline preprint information.
- [#245](https://github.com/nf-core/mag/pull/245) - Add Prokka to annotate binned genomes.

### `Changed`

- [#249](https://github.com/nf-core/mag/pull/249) - Update workflow overview figure.
- [#258](https://github.com/nf-core/mag/pull/258) - Updated MultiQC 1.9 to 1.11.
- [#260](https://github.com/nf-core/mag/pull/260) - Updated SPAdes 3.13.1 -> 3.15.3, MEGAHIT 1.2.7 -> 1.2.7

### `Fixed`

- [#256](https://github.com/nf-core/mag/pull/256) - Fix `--skip_busco`.
- [#236](https://github.com/nf-core/mag/pull/236) - Fix large assemblies (> 4 billion nucleotides in length).
- [#254](https://github.com/nf-core/mag/pull/254) - Fix MetaBAT2 error with nextflow version 21.10.x (21.04.03 is the latest functional version for nf-core/mag 2.1.0).
- [#255](https://github.com/nf-core/mag/pull/255) - Update gtdbtk conda channel.
- [#258](https://github.com/nf-core/mag/pull/258) - FastP results are now in MultiQC.

## v2.1.0 - 2021/07/29

### `Added`

- [#212](https://github.com/nf-core/mag/pull/212), [#214](https://github.com/nf-core/mag/pull/214) - Add bin abundance estimation based on median sequencing depths of corresponding contigs (results are written to `results/GenomeBinning/bin_depths_summary.tsv` and `results/GenomeBinning/bin_summary.tsv`) [#197](https://github.com/nf-core/mag/issues/197).
- [#214](https://github.com/nf-core/mag/pull/214) - Add generation of (clustered) heat maps with bin abundances across samples (using centered log-ratios)
- [#217](https://github.com/nf-core/mag/pull/217) - Publish genes predicted with Prodigal within BUSCO run (written to `results/GenomeBinning/QC/BUSCO/[assembler]-[bin]_prodigal.gff`).

### `Changed`

- [#218](https://github.com/nf-core/mag/pull/218) - Update to nf-core 2.0.1 `TEMPLATE` (DSL2)

### `Fixed`

- [#226](https://github.com/nf-core/mag/pull/226) - Fix handling of `BUSCO` output when run in auto lineage selection mode and selected specific lineage is the same as the generic one.

## v2.0.0 - 2021/06/01

### `Added`

- [#179](https://github.com/nf-core/mag/pull/179) - Add BUSCO automated lineage selection functionality (new default). The pameter `--busco_auto_lineage_prok` can be used to only consider prokaryotes and the parameter `--busco_download_path` to run BUSCO in `offline` mode.
- [#178](https://github.com/nf-core/mag/pull/178) - Add taxonomic bin classification with `GTDB-Tk` `v1.5.0` (for bins filtered based on `BUSCO` QC metrics).
- [#196](https://github.com/nf-core/mag/pull/196) - Add process for CAT database creation as an alternative to using pre-built databases.

### `Changed`

- [#162](https://github.com/nf-core/mag/pull/162) - Switch to DSL2
- [#162](https://github.com/nf-core/mag/pull/162) - Changed `--input` file format from `TSV` to `CSV` format, requires header now
- [#162](https://github.com/nf-core/mag/pull/162) - Update `README.md`, `docs/usage.md` and `docs/output.md`
- [#162](https://github.com/nf-core/mag/pull/162) - Update `FastP` from version `0.20.0` to `0.20.1`
- [#162](https://github.com/nf-core/mag/pull/162) - Update `Bowtie2` from version `2.3.5` to `2.4.2`
- [#162](https://github.com/nf-core/mag/pull/162) - Update `FastQC` from version `0.11.8` to `0.11.9`
- [#172](https://github.com/nf-core/mag/pull/172) - Compressed discarded MetaBAT2 output files
- [#176](https://github.com/nf-core/mag/pull/176) - Update CAT DB link
- [#179](https://github.com/nf-core/mag/pull/179) - Update `BUSCO` from version `4.1.4` to `5.1.0`
- [#179](https://github.com/nf-core/mag/pull/179) - By default BUSCO now performs automated lineage selection instead of using the bacteria_odb10 lineage as reference. Specific lineage datasets can still be provided via `--busco_reference`.
- [#178](https://github.com/nf-core/mag/pull/178) - Change output file: `results/GenomeBinning/QC/quast_and_busco_summary.tsv` -> `results/GenomeBinning/bin_summary.tsv`, contains GTDB-Tk results as well.
- [#191](https://github.com/nf-core/mag/pull/191) - Update to nf-core 1.14 `TEMPLATE`
- [#193](https://github.com/nf-core/mag/pull/193) - Compress CAT output files [#180](https://github.com/nf-core/mag/issues/180)
- [#198](https://github.com/nf-core/mag/pull/198) - Requires nextflow version `>= 21.04.0`
- [#200](https://github.com/nf-core/mag/pull/200) - Small changes in GitHub Actions tests
- [#203](https://github.com/nf-core/mag/pull/203) - Renamed `fastp` params and improved description in documentation: `--mean_quality` -> `--fastp_qualified_quality`, `--trimming_quality` -> `--fastp_cut_mean_quality`

### `Fixed`

- [#175](https://github.com/nf-core/mag/pull/175) - Fix bug in retrieving the `--max_unbinned_contigs` longest unbinned sequences that are longer than `--min_length_unbinned_contigs` (`split_fasta.py`)
- [#175](https://github.com/nf-core/mag/pull/175) - Improved runtime of `split_fasta.py` in `METABAT2` process (important for large assemblies, e.g. when computing co-assemblies)
- [#194](https://github.com/nf-core/mag/pull/194) - Allow different folder structures for Kraken2 databases containing `*.k2d` files [#187](https://github.com/nf-core/mag/issues/187)
- [#195](https://github.com/nf-core/mag/pull/195) - Fix documentation regarding required compression of input FastQ files [#160](https://github.com/nf-core/mag/issues/160)
- [#196](https://github.com/nf-core/mag/pull/196) - Add process for CAT database creation as solution for problem caused by incompatible `DIAMOND` version used for pre-built `CAT database` and `CAT classification` [#90](https://github.com/nf-core/mag/issues/90), [#188](https://github.com/nf-core/mag/issues/188)

## v1.2.0 - 2021/02/10

### `Added`

- [#146](https://github.com/nf-core/mag/pull/146) - Add `--coassemble_group` parameter to allow group-wise co-assembly
- [#146](https://github.com/nf-core/mag/pull/146) - Add `--binning_map_mode` parameter allowing different mapping strategies to compute co-abundances used for binning (`all`, `group`, `own`)
- [#149](https://github.com/nf-core/mag/pull/149) - Add two new parameters to allow custom SPAdes and MEGAHIT options (`--spades_options` and `--megahit_options`)

### `Changed`

- [#141](https://github.com/nf-core/mag/pull/141) - Update to nf-core 1.12.1 `TEMPLATE`
- [#143](https://github.com/nf-core/mag/pull/143) - Manifest file has to be handed over via `--input` parameter now
- [#143](https://github.com/nf-core/mag/pull/143) - Changed format of manifest input file: requires a '.tsv' suffix and additionally contains group ID
- [#143](https://github.com/nf-core/mag/pull/143) - TSV `--input` file allows now also entries containing only short reads
- [#145](https://github.com/nf-core/mag/pull/145) - When using TSV input files, uses sample IDs now for `FastQC` instead of basenames of original read files. Allows non-unique file basenames.

### `Removed`

- [#143](https://github.com/nf-core/mag/pull/143) - Change parameter: `--manifest` -> `--input`

## v1.1.2 - 2020/11/24

### `Changed`

- [#135](https://github.com/nf-core/mag/pull/135) - Update to nf-core 1.12 `TEMPLATE`

### `Fixed`

- [#133](https://github.com/nf-core/mag/pull/133) - Fixed processing of `--input` parameter [#131](https://github.com/nf-core/mag/issues/131)

## v1.1.1 - 2020/11/10

### `Added`

- [#121](https://github.com/nf-core/mag/pull/121) - Add full-size test
- [#124](https://github.com/nf-core/mag/pull/124) - Add worfklow overview figure to `README`

### `Changed`

- [#123](https://github.com/nf-core/mag/pull/123) - Update to new nf-core 1.11 `TEMPLATE`

### `Fixed`

- [#118](https://github.com/nf-core/mag/pull/118) - Fix `seaborn` to `v0.10.1` to avoid `nanoplot` error
- [#120](https://github.com/nf-core/mag/pull/120) - Fix link to CAT database in help message
- [#124](https://github.com/nf-core/mag/pull/124) - Fix description of `CAT` process in `output.md`

## v1.1.0 - 2020/10/06

### `Added`

- [#35](https://github.com/nf-core/mag/pull/35) - Add social preview image
- [#49](https://github.com/nf-core/mag/pull/49) - Add host read removal with `Bowtie 2` and according custom section to `MultiQC`
- [#49](https://github.com/nf-core/mag/pull/49) - Add separate `MultiQC` section for `FastQC` after preprocessing
- [#65](https://github.com/nf-core/mag/pull/65) - Add `MetaBAT2` RNG seed parameter `--metabat_rng_seed` and set the default to 1 which ensures reproducible binning results
- [#65](https://github.com/nf-core/mag/pull/65) - Add parameters `--megahit_fix_cpu_1`, `--spades_fix_cpus` and `--spadeshybrid_fix_cpus` to ensure reproducible results from assembly tools
- [#66](https://github.com/nf-core/mag/pull/66) - Export `depth.txt.gz` into result folder
- [#67](https://github.com/nf-core/mag/pull/67) - Compress assembly files
- [#82](https://github.com/nf-core/mag/pull/82) - Add `nextflow_schema.json`
- [#104](https://github.com/nf-core/mag/pull/104) - Add parameter `--save_busco_reference`

### `Changed`

- [#56](https://github.com/nf-core/mag/pull/56) - Update `MetaBAT2` from `v2.13` to `v2.15`
- [#46](https://github.com/nf-core/mag/pull/46) - Update `MultiQC` from `v1.7` to `v1.9`
- [#88](https://github.com/nf-core/mag/pull/88) - Update to new nf-core 1.10.2 `TEMPLATE`
- [#88](https://github.com/nf-core/mag/pull/88) - `--reads` is now removed, use `--input` instead
- [#101](https://github.com/nf-core/mag/pull/101) - Prevented PhiX alignments from being stored in work directory [#97](https://github.com/nf-core/mag/issues/97)
- [#104](https://github.com/nf-core/mag/pull/104), [#111](https://github.com/nf-core/mag/pull/111) - Update `BUSCO` from `v3.0.2` to `v4.1.4`

### `Fixed`

- [#29](https://github.com/nf-core/mag/pull/29) - Fix `MetaBAT2` binning discards unbinned contigs [#27](https://github.com/nf-core/mag/issues/27)
- [#31](https://github.com/nf-core/mag/pull/31), [#36](https://github.com/nf-core/mag/pull/36), [#76](https://github.com/nf-core/mag/pull/76), [#107](https://github.com/nf-core/mag/pull/107) - Fix links in README
- [#47](https://github.com/nf-core/mag/pull/47) - Fix missing `MultiQC` when `--skip_quast` or `--skip_busco` was specified
- [#49](https://github.com/nf-core/mag/pull/49), [#89](https://github.com/nf-core/mag/pull/89) - Added missing parameters to summary
- [#50](https://github.com/nf-core/mag/pull/50) - Fix missing channels when `--keep_phix` is specified
- [#54](https://github.com/nf-core/mag/pull/54) - Updated links to `minikraken db`
- [#54](https://github.com/nf-core/mag/pull/54) - Fixed `Kraken2` dp preparation: allow different names for compressed archive file and contained folder as for some minikraken dbs
- [#55](https://github.com/nf-core/mag/pull/55) - Fixed channel joining for multiple samples causing `MetaBAT2` error [#32](https://github.com/nf-core/mag/issues/32)
- [#57](https://github.com/nf-core/mag/pull/57) - Fix number of threads used by `MetaBAT2` program `jgi_summarize_bam_contig_depths`
- [#70](https://github.com/nf-core/mag/pull/70) - Fix `SPAdes` memory conversion issue [#61](https://github.com/nf-core/mag/issues/61)
- [#71](https://github.com/nf-core/mag/pull/71) - No more ignoring errors in `SPAdes` assembly
- [#72](https://github.com/nf-core/mag/pull/72) - No more ignoring of `BUSCO` errors
- [#73](https://github.com/nf-core/mag/pull/73), [#75](https://github.com/nf-core/mag/pull/75) - Improved output documentation
- [#96](https://github.com/nf-core/mag/pull/96) - Fix missing bin names in `MultiQC` BUSCO section [#78](https://github.com/nf-core/mag/issues/78)
- [#104](https://github.com/nf-core/mag/pull/104) - Fix `BUSCO` errors causing missing summary output [#77](https://github.com/nf-core/mag/issues/77)

### `Deprecated`

- [#29](https://github.com/nf-core/mag/pull/29) - Change depreciated parameters: `--singleEnd` -> `--single_end`, `--igenomesIgnore` -> `--igenomes_ignore`

## v1.0.0 - 2019/12/20

Initial release of nf-core/mag, created with the [nf-core](http://nf-co.re/) template.

### `Added`

- short and long reads QC (fastp, porechop, filtlong, fastqc)
- Lambda and PhiX detection and filtering (bowtie2, nanolyse)
- Taxonomic classification of reads (centrifuge, kraken2)
- Short read and hybrid assembly (megahit, metaspades)
- metagenome binning (metabat2)
- QC of bins (busco, quast)
- annotation (cat/bat)
