Skip to content

Latest commit

 

History

History
106 lines (68 loc) · 4.55 KB

CHANGELOG.md

File metadata and controls

106 lines (68 loc) · 4.55 KB
Raw

nf-core/bamtofastq: Changelog

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

v2.1.1 - Joy Buolamwini

Added

  • #73 Sync TEMPLATE with tools 2.12
  • #75, #78 Sync TEMPLATE with tools 2.13
  • #80, #84 Sync TEMPLATE with tools 2.13.1

Changed

  • #74 Update to samtools to v1.19.2
  • #76 Update modules cat/fastq and samtools/view
  • #88 Update subworkflow utils_nfcore_pipeline

Fixed

  • #77 Fix detection of paired-end or single-end for input with less than 1000 reads
  • #81 Add function getGenomeAttribute to main.nf and remove it from subworkflows/local/utils_nfcore_bamtofastq_pipeline/main.nf

Dependencies

Dependency Old version New version
Samtools 1.17 1.19.2
MultiQC 1.15 1.21

v2.1.0 - Grace Hopper

Added

  • #61 Sync TEMPLATE with tools 2.9
  • #64 Sync TEMPLATE with tools 2.10

Changed

  • #63 Replace extract_csv with nf-validation plugin

Fixed

  • #62 Adjust subway map for dark mode.

Dependencies

Dependency Old version New version
MultiQC 1.14 1.15

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.