nf-core/bamtofastq

Converts bam or cram files to fastq format and does quality control.

bamtofastqconversioncramtofastq

Launch version 2.1.1 https://github.com/nf-core/bamtofastq

Version history

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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

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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

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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

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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

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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

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Initial release of qbic-pipelines/bamtofastq!