nf-core/bamtofastq
Converts bam or cram files to fastq format and does quality control.
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!
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