nf-core/eager: [2.1.0] - Ravensburg - 2020-03-05

[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/)

• #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

• 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