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[2.1.0] - Ravensburg - 2020-03-05
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@apeltzer apeltzer released this 05 Mar 15:42
· 1847 commits to master since this release
2.1.0
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[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
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