# nf-core/circdna: 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).

## v1.0.3 - [2023-03-23]

### `Added`

- documentation about absolute path needed of AmpliconArchitect data repository
- ampliconclassifier stub run tests
- new version of circdna metromap with updated colors
- Circle-Map Realign error message output. Added a new error message to circle_map realign to identify errors more quickly.

### `Fixed`

- Circle_finder bug with bash sort command wanting to write into /tmp/ directory and not into work directory

### `Dependencies`

### `Deprecated`

## v1.0.2 - [2023-03-07]

### `Added`

- ampliconclassifier/makeinput module added -> Generates the input file used for ampliconclassifier functions
- ampliconclassifier/makeresultstable added -> Generates results table from AmpliconArchitect and AmpliconClassifier
- CNN Reference File For AmpliconArchitect
- mm10 option for AmpliconArchitect
- stub runs for AmpliconArchitect processes
- New module versions
- nf-core template 2.7.2

### `Fixed`

- Fixed ZeroDivisionError by Circle-Map
- Fixed keep_duplicates and skip_markduplicates parameter bug

### `Dependencies`

### `Deprecated`

- AmpliconArchitect Summary Process was deprecated

## v1.0.1 - [2022-06-22]

### `Added`

- Documentation Updates

### `Fixed`

- Fixed Bug with pipeline version in nextflow.config
- Fixed Circle-Map Realign bug in which only one sample is processed

### `Dependencies`

### `Deprecated`

- Samtools FAIDX

## v1.0.0 - [2022-06-01]

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

nf-core/circdna is a bioinformatics analysis pipeline for the identification of circular DNAs in eukaryotic cells. The pipeline is able to process WGS, ATAC-seq data or Circle-Seq data to give insights into the circular DNA landscape in your samples.

In total, the user can choose between 5 different branches inside the pipeline, depending on the biological question and the input data set. In these branches, specific software is used that is built for either the identification of amplified circular DNAs, the detection of putative circular DNA junctions, or the de novo assembly and mapping of circular DNAs.
