Releases: nf-core/eager
Releases · 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
--preserve5pfunction 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
[2.0.7] - 2019-06-10
Added
- #189 - Outputing unmapped reads in a fastq files with the --strip_input_fastq flag
- #186 - Make FastQC skipping [possible]
/(#182) - 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
- #152 - DamageProfiler errors won't crash entire pipeline anymore
- #176 - Increase runtime for DamageProfiler on large reference genomes
- #172 - DamageProfiler errors won't crash entire pipeline anymore
- #174 - Publish DeDup files properly
- #196 - Fix reference issues
- #196 - Fix issues with PE data being mapped incompletely
- #200 - Fix minor issue with some typos
- #210 - Fix PMDTools encoding issue from
samtools calmdgenerated files by running throughsa]mtools viewfirst - #221 - Fix BWA Index not being reused by multiple samples
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]
[2.0.6] - 2019-03-05
Added
- #152 - Clarified
--complexity_filterflag 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
- #151 - Fixed [post-deduplication step errors](#128
- #147 - Fix Samtools Index for large references
- #145 - Added Picard Memory Handling fix
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
[2.0.5] - 2019-01-30
Added
- #127 - Added a second testcase for testing the pipeline properly
- #129 - Support BAM files as input format
- #131 - Support different reference genome file extensions
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
Release [2.0.4] - 2019-01-09
Added
- #111 - Allow Zipped FastA reference input
- #113 - All files are now staged via channels, which is considered best practice by Nextflow
- #114 - Add proper runtime defaults for multiple processes
- #118 - Add centralized configs handling by https://github.com/nf-core/configs
- #115 - Add DamageProfiler MultiQC support
- #122 - Pull Dockerhub image again
Fixed
- #110 - Fix for MultiQC Missing Second FastQC report
- #112 - Remove redundant UDG options
2.0.3
[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
- #84 - Fix for Samtools index issues
- #96 - Fix for MarkDuplicates issues found by @nilesh-tawari
Other
- Added Slack button to repository readme
2.0.2
2.0.1
2.0.0 - "Kaufbeuren"
2.0 "Kaufbeuren" - 2018-10-17
Initial release of nf-core/eager featuring:
- 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.