2.1.1 - Joy Buolamwini

What's Changed

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

New Contributors

• @allaway made their first contribution in #68
• @asp8200 made their first contribution in #74

Full Changelog: 2.1.0...2.1.1

2.1.0 - Grace Hopper

What's Changed

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

New Contributors

• @maxulysse made their first contribution in #66

Full Changelog: 2.0.0...2.1.0

2.0.0 - Annie Easley

What's Changed

• Porting pipeline to DSL2 and to nf-core
• Add igenomes by @SusiJo in #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 #46

Full Changelog: 1.2.0...2.0.0

1.2.0 - Anna Winlock

What's Changed

• 🏃‍♂️ Improve runtime:
  - speed improvements by @ggabernet in #31
  - added samtools_collate_fast and changed cat command by @SusiJo in #32
  - added new flag --reads_in_memory by @SusiJo in #33
• 📁 Support for CRAM files:
  - Add support for CRAM files by @BrunoGrandePhD in #36

New Contributors

• @ggabernet made their first contribution in #31
• @BrunoGrandePhD made their first contribution in #36

Full Changelog: 1.1.0...1.2.0

1.1.0 - Katherine Johnson

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

1.0.0 - Ada Lovelace

Initial release of qbic-pipelines/bamtofastq!