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nf-core/circdna: Changelog

The format is based on Keep a Changelog and this project adheres to Semantic Versioning.

v1.1.0 - [2024-02-03]

Credits

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

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

v1.0.4 - [2023-06-26]

Added

Fixed

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

Dependencies

Deprecated

v1.0.3 - [2023-05-26]

Added

  • Licence, contact, source information for AmpliconArchitect and PrepareAA python scripts
  • documentation about absolute path needed of AmpliconArchitect data repository
  • 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
  • nf-core template update 2.8

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

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 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.