CHANGELOG.md

nf-core/bamtofastq: Changelog

The format is based on Keep a Changelog and this project adheres to Semantic Versioning.

v2.1.0dev

Added

• #61 Sync TEMPLATE with tools 2.9

Changed

• #63 Replace extract_csv with nf-validation plugin

Fixed

• #62 Adjust subway map for dark mode.

Dependencies

Dependency	Old version	New version

Deprecated

v2.0.0 - Annie Easley

Initial release of nf-core/bamtofastq, created with the nf-core template.

Added

• #49 Add descriptions to main options
• #48 Add igenomes
• #45 Add test.yml files with md5sums
• #44 DSL2 conversion

Changed

• #55 Code review suggestions & formatting
• #54 Code review changes
• #53 Code review & updated modules
• #52 Code review changed resources in configs
• #47 Sync TEMPLATE with tools 2.8

Fixed

• #49 Fixed release version
• #45 Minor bugfix with chromosome extraction

Dependencies

Dependency	Old version	New version
multiqc	1.9	1.14
samtools	1.10	1.17

Deprecated

• Option --cram_files not needed anymore due to automatic format detection.

v1.2.0 - Anna Winlock

• #36 Add options --cram_files and --reference_fasta to add support for CRAM files.
• #31 Add option --samtools_collate_fast and improve speed of cat.
• #32 Added --samtools_collate_fast to sortExtractMapped and changed cat command to append.
• #33 Added flag --reads_in_memory to specify how many reads shall be stored in memory.

v1.1.0 - Katherine Johnson

• #21 Allows bam indices as additional input files
• #23 Fix documentation: --bam is --input now
• #23 Make stats computation optional with parameter --no_stats. Use at own risk.
• #26 BAM index is now also used for processes dealing with separating reads based on the mapping status of both mates

v1.0.0 - Ada Lovelace

Initial release of qbic-pipelines/bamtofastq, created with the nf-core template.