v 1.1.0 - 2024-02-10 - Tremendous Wombat

v1.1.0 - [2024-02-10]

Credits

Special thanks to the following for their input and contributions to the release:

• Jens Luebeck
• Simon Pearce
• Maxime U Garcia
• Alex M. Ascensión

Enhancements & fixes

• Nf-core template update to 2.11.1
  • update of nf-core modules versions
• Removed AmpliconArchitect and AmpliconClassifier modules with their respective scripts in /bin
  • AmpliconArchitect and AmpliconClassifier is now run inside the AmpliconSuite-Pipeline. Additional scripts are not necessary.
  • Removed respective configs and workflow code
• Added AmpliconSuite-Pipeline
  • A wrapper for calling copy numbers, preparing amplified intervals, running AmpliconArchitect, and calling amplicon classes using AmpliconClassifier
  • Added docker container named PrepareAA to run AmpliconSuite-Pipeline with singualarity or docker
  • Added module configs and description
• Changed assets/multiqc_config.ymlto fit new pipeline version
• Included directory checks for mosek_license_dir and aa_data_repo .
  • Removed both directory parameters in the test profile as it is only checked when running ampliconarchitect
• Updated nextflow_schema.json to give better details about how to use --circle_identifier
• made --circle_identifier an essential parameter
• made --input_format an essential parameter and removed the default value to request specification by user
• Updated --bwa_index to accept only directory paths to the bwa index files. Makes the user input easier to not need to deal with file endings and patterns. Bug identified by Alex M. Ascensión in #68

v 1.0.4 - 2023-06-05 - Patched Golden Wombat

v1.0.4 - 2023-06-06 - Patched Golden Wombat - Patch Release to Fix v 1.0.3 [2023-06-26]

Added

Fixed

• Bug that the pipeline only runs with one sample when Picard Markduplicates is used

Dependencies

Deprecated

v 1.0.3 - 2023-06-05 - Golden Wombat

v1.0.3 - [2023-06-05] - Golden Wombat

Added

• Licence, contact, source information for AmpliconArchitect and PrepareAA python scripts - Recommendation by @SPPearce
• documentation about absolute path needed of AmpliconArchitect data repository - Recommendation by @SPPearce
• ampliconclassifier stub run tests
• new version of circdna metromap with updated colors
• note that ATAC-seq should be used in caution with the pipeline.
• build docker container for prepareaa -> Needs to be built first and will be included in the next release - Thanks to @ewels
• nf-core template update 2.8 - Thanks to the nf-core team
• newest versions of AmpliconArchitect - Recommendation and help from @jluebeck

Fixed

• Circle_finder bug with bash sort command wanting to write into /tmp/ directory and not into work directory
• Usage.md updated to new paths and addition of nf-core modules

Dependencies

Deprecated

• Local python scripts not included in the pipeline
• Local versions of nf-core modules

Acknowledgements

Thanks to the reviewers @jluebeck and @SPPearce for providing relevant feedback for improvements and clarity of nf-core/circdna. Also thanks to @ewels for the comprehensive help in building the docker image for PrepareAA for future releases.

v 1.0.3dev-alpha - 2023-05-17 - Ingenious Wombat

Updated Dockerfile to release docker image for PrepareAA.

v 1.0.3dev - 2023-05-17 - Curious Wombat

Dev release to push Docker container containing PrepareAA python dependencies.

v 1.0.2 - 2023-03-09 - Bronze Pigeon

v1.0.2 - [2023-03-09] - Bronze Pigeon

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

v 1.0.1 - 2022-06-22 - Black Bronze Viper

v1.0.1 - [2022-06-22] - Black Bronze Viper

In this Release, a bug was fixed in the nextflow.config and the documentation was updated.

Added

• Documentation Updates

Fixed

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

Deprecated

• Samtools FAIDX

v 1.0.0 - 2022-06-01 - Stone Green Lizard

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.