What’s Changed

• Added fastqutils/info to check for truncated or quality-mismatched files by @famosab in https://github.com/nf-core/bamtofastq/pull/120
• Convert the pipeline-level pytest tests to nf-test and use them for CI testing by @maxulysse and @famosab in https://github.com/nf-core/bamtofastq/pull/108, https://github.com/nf-core/bamtofastq/pull/110 and https://github.com/nf-core/bamtofastq/pull/112
• Various template updates by @asp8200 and @maxulysse and final template update to the latest version 3.3.1 by @famosab in https://github.com/nf-core/bamtofastq/pull/128

New Contributors

• @famosab made their first contribution in https://github.com/nf-core/bamtofastq/pull/108

Full Changelog: https://github.com/nf-core/bamtofastq/compare/2.1.1...2.2.0

What’s Changed

• tweak usage.md by @allaway in https://github.com/nf-core/bamtofastq/pull/68
• Important! Template update for nf-core/tools v2.12 by @nf-core-bot in https://github.com/nf-core/bamtofastq/pull/73
• Update samtools by @asp8200 in https://github.com/nf-core/bamtofastq/pull/74
• Nf core template merge 2.13 resolve conflicts by @asp8200 in https://github.com/nf-core/bamtofastq/pull/78
• Important! Template update for nf-core/tools v2.13.1 by @nf-core-bot in https://github.com/nf-core/bamtofastq/pull/80
• Fixing less than 1000 reads issue by @asp8200 in https://github.com/nf-core/bamtofastq/pull/77
• update all modules by @asp8200 in https://github.com/nf-core/bamtofastq/pull/76
• Add fct getGenomeAttribute to main.nf by @asp8200 in https://github.com/nf-core/bamtofastq/pull/81
• Update changelog for release v2.1.1 by @asp8200 in https://github.com/nf-core/bamtofastq/pull/82
• Removing option stub from CI-test of download by @asp8200 in https://github.com/nf-core/bamtofastq/pull/84
• Import fasta_fai in main.nf by @asp8200 in https://github.com/nf-core/bamtofastq/pull/85
• feat(subworkflow): update utils_nfcore_pipeline by @maxulysse in https://github.com/nf-core/bamtofastq/pull/88
• Release v2.1.1 by @asp8200 in https://github.com/nf-core/bamtofastq/pull/83

New Contributors

• @allaway made their first contribution in https://github.com/nf-core/bamtofastq/pull/68
• @asp8200 made their first contribution in https://github.com/nf-core/bamtofastq/pull/74

Full Changelog: https://github.com/nf-core/bamtofastq/compare/2.1.0...2.1.1

What’s Changed

• Post-release version bump by @SusiJo in https://github.com/nf-core/bamtofastq/pull/59
• Important! Template update for nf-core/tools v2.9 by @nf-core-bot in https://github.com/nf-core/bamtofastq/pull/61
• Fix subway map by @SusiJo in https://github.com/nf-core/bamtofastq/pull/62
• Deploy nf-validation plugin by @SusiJo in https://github.com/nf-core/bamtofastq/pull/63
• Important! Template update for nf-core/tools v2.10 by @nf-core-bot in https://github.com/nf-core/bamtofastq/pull/64
• CHORES: Prepare Release 2.1.0 by @maxulysse in https://github.com/nf-core/bamtofastq/pull/66
• Candidate Release 2.1.0 by @maxulysse in https://github.com/nf-core/bamtofastq/pull/65

New Contributors

• @maxulysse made their first contribution in https://github.com/nf-core/bamtofastq/pull/66

Full Changelog: https://github.com/nf-core/bamtofastq/compare/2.0.0...2.1.0

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!