Version history

What's Changed

* Porting pipeline to DSL2 and to nf-core

* Add igenomes by @SusiJo in https://github.com/nf-core/bamtofastq/pull/48

* --cram_files parameter is deprecated as file type is automatically detected

* --index_files parameter is deprecated and if no index files are provided in the samplesheet, they will be generated

* --input changed to samplesheet and does not take paths to data anymore

New Contributors

* @nf-core-bot made their first contribution in https://github.com/nf-core/bamtofastq/pull/46

*Full Changelog*: https://github.com/nf-core/bamtofastq/compare/1.2.0...2.0.0

What's Changed

  • 🏃‍♂️ Improve runtime:

       - speed improvements by @ggabernet in https://github.com/qbic-pipelines/bamtofastq/pull/31
       - added samtools_collate_fast and changed cat command by @SusiJo in https://github.com/qbic-pipelines/bamtofastq/pull/32
       - added new flag --reads_in_memory by @SusiJo in https://github.com/qbic-pipelines/bamtofastq/pull/33
    
  • 📁 Support for CRAM files:

        - Add support for CRAM files by @BrunoGrandePhD in https://github.com/qbic-pipelines/bamtofastq/pull/36
        
    

New Contributors

* @ggabernet made their first contribution in https://github.com/qbic-pipelines/bamtofastq/pull/31

* @BrunoGrandePhD made their first contribution in https://github.com/qbic-pipelines/bamtofastq/pull/36

*Full Changelog*: https://github.com/qbic-pipelines/bamtofastq/compare/1.1.0...1.2.0

New features

* Allows to provide bam indices as additional input to prevent re-computation

* All stats can be skipped, speeding up computation, with --no_stats

Initial release of qbic-pipelines/bamtofastq!