Skip to content

Latest commit

 

History

History
205 lines (148 loc) · 11.2 KB

CHANGELOG.md

File metadata and controls

205 lines (148 loc) · 11.2 KB
Raw

nf-core/eager: Changelog

All notable changes to this project will be documented in this file.

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

[2.1.0] - Ravensburg - 2020-03-05

Added

  • Added Support for automated tests using GitHub Actions, replacing travis
  • #40, #231 - Added genotyping capability through GATK UnifiedGenotyper (v3.5), GATK HaplotypeCaller (v4.1) and FreeBayes
  • Added MultiVCFAnalyzer module
  • #240 - Added human sex determination module
  • #226 - Added --preserve5p function for AdapterRemoval
  • #212 - Added ability to use only mergedreads downstream from Adapterremoval
  • #265 - Adjusted full markdown linting in Travis CI
  • #247 - Added nuclear contamination with angsd
  • #258 - Added ability to report bedtools stats to features (e.g. depth/breadth of annotated genes)
  • #249 - Added metagenomic classification of unmapped reads with MALT and aDNA authentication with MaltExtract
  • #302 - Added mitochondrial to nuclear ratio calculation
  • #302 - Added VCF2Genome for concensus sequence generation
  • Fancy new logo from ZandraFagernas
  • #286 - Adds pipeline-specific profiles (loaded from nf-core configs)
  • #310 - Generalises base.config
  • #326 - Add Biopython and xopen dependencies
  • #336 - Change default Y-axis maximum value of DamageProfiler to 30% to match popular (but slower) mapDamage, and allow user to set their own value.
  • #352 - Add social preview image
  • #355 - Add Kraken2 metagenomics classifier
  • #90 - Added endogenous DNA calculator (original repository: https://github.com/aidaanva/endorS.py/)

Fixed

  • #227 - Large re-write of input/output process logic to allow maximum flexibility. Originally to address #227, but further expanded
  • Fixed Travis-Ci.org to Travis-Ci.com migration issues
  • #266 - Added sanity checks for input filetypes (i.e. only BAM files can be supplied if --bam)
  • #237 - Fixed and Updated script scrape_software_versions
  • #322 - Move extract map reads fastq compression to pigz
  • #327 - Speed up strip_input_fastq process and make it more robust
  • #342 - Updated to match nf-core tools 1.8 linting guidelines
  • #339 - Converted unnecessary zcat + gzip to just cat for a performance boost
  • #344 - Fixed pipeline still trying to run when using old nextflow version

Dependencies

  • adapterremoval=2.2.2 upgraded to 2.3.1
  • adapterremovalfixprefix=0.0.4 upgraded to 0.0.5
  • damageprofiler=0.4.3 upgraded to 0.4.9
  • angsd=0.923 upgraded to 0.931
  • gatk4=4.1.2.0 upgraded to 4.1.4.1
  • mtnucratio=0.5 upgraded to 0.6
  • conda-forge::markdown=3.1.1 upgraded to 3.2.1
  • bioconda::fastqc=0.11.8 upgraded to 0.11.9
  • bioconda::picard=2.21.4 upgraded to 2.22.0
  • bioconda::bedtools=2.29.0 upgraded to 2.29.2
  • pysam=0.15.3 upgraded to 0.15.4
  • conda-forge::pandas=1.0.0 upgraded to 1.0.1
  • bioconda::freebayes=1.3.1 upgraded to 1.3.2
  • conda-forge::biopython=1.75 upgraded to 1.76

[2.0.7] - 2019-06-10

Added

  • #189 - Outputting unmapped reads in a fastq files with the --strip_input_fastq flag
  • #186 - Make FastQC skipping possible
  • Merged in nf-core/tools release V1.6 template changes
  • A lot more automated tests using Travis CI
  • Don't ignore DamageProfiler errors anymore
  • #220 - Added post-mapping filtering statistics module and corresponding MultiQC statistics #217

Fixed

Dependencies

  • Added DeDup v0.12.5 (json support)
  • Added mtnucratio v0.5 (json support)
  • Updated Picard 2.18.27 -> 2.20.2
  • Updated GATK 4.1.0.0 -> 4.1.2.0
  • Updated damageprofiler 0.4.4 -> 0.4.5
  • Updated r-rmarkdown 1.11 -> 1.12
  • Updated fastp 0.19.7 -> 0.20.0
  • Updated qualimap 2.2.2b -> 2.2.2c

[2.0.6] - 2019-03-05

Added

  • #152 - Clarified --complexity_filter flag to be specifically for poly G trimming.
  • #155 - Added Dedup log to output folders
  • #159 - Added Possibility to skip AdapterRemoval, skip merging, skip trimming fixing #64,#137 - thanks to @maxibor, @jfy133

Fixed

Dependencies

  • Picard Tools 2.18.23 -> 2.18.27
  • GATK 4.0.12.0 -> 4.1.0.0
  • FastP 0.19.6 -> 0.19.7

[2.0.5] - 2019-01-28

Added

Fixed

  • #128 - Fixed reference genome handling errors

Dependencies

  • Picard Tools 2.18.21 -> 2.18.23
  • R-Markdown 1.10 -> 1.11
  • FastP 0.19.5 -> 0.19.6

[2.0.4] - 2019-01-09

Added

Fixed

[2.0.3] - 2018-12-12

Added

  • #80 - BWA Index file handling
  • #77 - Lots of documentation updates by @jfy133
  • #81 - Renaming of certain BAM options
  • #92 - Complete restructure of BAM options

Fixed

Other

  • Added Slack button to repository readme

[2.0.2] - 2018-11-03

Changed

  • #70 - Uninitialized readPaths warning removed

Added

  • #73 - Travis CI Testing of Conda Environment added

Fixed

  • #72 - iconv Issue with R in conda environment

[2.0.1] - 2018-11-02

Fixed

  • #69 - FastQC issues with conda environments

[2.0.0] "Kaufbeuren" - 2018-10-17

Initial release of nf-core/eager:

Added

  • FastQC read quality control
  • (Optional) Read complexity filtering with FastP
  • Read merging and clipping using AdapterRemoval v2
  • Mapping using BWA / BWA Mem or CircularMapper
  • Library Complexity Estimation with Preseq
  • Conversion and Filtering of BAM files using Samtools
  • Damage assessment via DamageProfiler, additional filtering using PMDTools
  • Duplication removal via DeDup
  • BAM Clipping with BamUtil for UDGhalf protocols
  • QualiMap BAM quality control analysis

Furthermore, this already creates an interactive report using MultiQC, which will be upgraded in V2.1 "Ulm" to contain more aDNA specific metrics.