# nf-core/nanoseq: 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).

## [2.0.0] - 2021-11-26

### Major enhancements

* Pipeline has been re-implemented in [Nextflow DSL2](https://www.nextflow.io/docs/latest/dsl2.html)
* Software containers are now obtained from [Biocontainers](https://biocontainers.pro/#/registry)
* Update pipeline template to nf-core/tools `2.1`
* [#77](https://github.com/nf-core/nanoseq/issues/77) - Skipped alignment steps
* [#97](https://github.com/nf-core/nanoseq/issues/97) - Add optional DNA cleaning option

### Parameters

* Added `--run_nanolyse` to run NanoLyse for DNA cleaning of FastQ files
* Added `--nanolyse_fasta` to provide a fasta file for nanolyse to filter against

### Software dependencies

| Dependency              | Old version | New version |
|-------------------------|-------------|-------------|
| `bioconductor-bambu`    | 1.0.0       | 1.0.2       |
| `nanolyse`              |             | 1.2.0       |
| `r-base`                | 4.0.3       | 4.0.2       |

> **NB:** Dependency has been __updated__ if both old and new version information is present.
> **NB:** Dependency has been __added__ if just the new version information is present.
> **NB:** Dependency has been __removed__ if version information isn't present.

## [1.1.0] - 2020-11-06

### Major enhancements

* Transcript reconstruction and quantification ([`bambu`](https://bioconductor.org/packages/release/bioc/html/bambu.html) or [`StringTie2`](https://ccb.jhu.edu/software/stringtie/) and [`featureCounts`](http://bioinf.wehi.edu.au/featureCounts/))
* Differential expression analysis at the gene-level ([`DESeq2`](https://bioconductor.org/packages/release/bioc/html/DESeq2.html)) and transcript-level ([`DEXSeq`](https://bioconductor.org/packages/release/bioc/html/DEXSeq.html))
* Ability to provide BAM input to the pipeline
* Change samplesheet format to be more flexible to BAM input files
* Add pycoQC and featureCounts output to MultiQC report
* Add AWS full-sized test data
* Add parameter JSON schema for pipeline
* Add citations file
* Update pipeline template to nf-core/tools `1.11`
* Collapsible sections for output files in `docs/output.md`
* Replace `set` with `tuple` and `file` with `path` in `input` section of all processes
* Capitalise process names
* Added `--gpus all` to Docker `runOptions` when using GPU as mentioned [here](https://github.com/docker/compose/issues/6691#issuecomment-514429646)
* Cannot invoke method `containsKey()` on null object when `--igenomes_ignore` is set [#76](https://github.com/nf-core/nanoseq/issues/76)

### Parameters

* Added `--barcode_both_ends` requires barcode on both ends for Guppy basecaller
* Added `--quantification_method` to specify the transcript quantification method to use
* Added `--skip_quantification` to skip transcript quantification and differential analysis
* Added `--skip_differential_analysis` to skip differential analysis with DESeq2 and DEXSeq
* Added `--publish_dir_mode` to customise method of publishing results to output directory [nf-core/tools#585](https://github.com/nf-core/tools/issues/585)

### Software dependencies

| Dependency              | Old version | New version |
|-------------------------|-------------|-------------|
| `Guppy`                 | 3.4.4       | 4.0.14      |
| `markdown`              | 3.1.1       | 3.3.3       |
| `multiqc`               | 1.8         | 1.9         |
| `nanoplot`              | 1.28.4      | 1.32.1      |
| `pygments`              | 2.5.2       | 2.7.2       |
| `pymdown-extensions`    | 6.0         | 8.0.1       |
| `python`                | 3.7.3       | 3.8.6       |
| `samtools`              | 1.9         | 1.11        |
| `ucsc-bedgraphtobigwig` | 357         | 377         |
| `ucsc-bedtobigbed`      | 357         | 377         |
| `bioconductor-bambu`    | -           | 1.0.0       |
| `bioconductor-bsgenome` | -           | 1.58.0      |
| `bioconductor-deseq2`   | -           | 1.30.0      |
| `bioconductor-dexseq`   | -           | 1.36.0      |
| `bioconductor-drimseq`  | -           | 1.18.0      |
| `bioconductor-stager`   | -           | 1.12.0      |
| `r-base`                | -           | 4.0.3       |
| `seaborn`               | -           | 0.10.1      |
| `stringtie`             | -           | 2.1.4       |
| `subread`               | -           | 2.0.1       |
| `psutil`                | -           | -           |

> **NB:** Dependency has been __updated__ if both old and new version information is present.
> **NB:** Dependency has been __added__ if just the new version information is present.
> **NB:** Dependency has been __removed__ if version information isn't present.

## [1.0.0] - 2020-03-05

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