The format is based on Keep a Changelog and this project adheres to Semantic Versioning.
- #654 - Fixed some values in JSON schema (used in launch GUI) not passing validation checks during run
- #655 - Updated read groups for all mappers to allow proper GATK validation
- Fixed issue with Docker container not being pullable by Nextflow due to version-number inconsistencies
- #640 - Added a pre-metagenomic screening filtering of low-sequence complexity reads with
bbduk
- #583 - Added
mapDamage2
rescaling of BAM files to remove damage - Updated usage (merging files) and workflow images reflecting new functionality.
- Removed leftover old DockerHub push CI commands.
- #627 - Added de Barros Damgaard citation to README
- #630 - Better handling of Qualimap memory requirements and error strategy.
- Fixed some incomplete schema options to ensure users supply valid input values
- #638 Fixed inverted circularfilter filtering (previously filtering would happen by default, not when requested by user as originally recorded in documentation)
- DeDup: Fixed Null Pointer Bug in DeDup by updating to 0.12.8 version
- #650 - Increased memory given to FastQC for larger files by making it multithreaded
- Update: DeDup v0.12.7 to v0.12.8
- Added large scale 'stress-test' profile for AWS (using de Barros Damgaard et al. 2018's 137 ancient human genomes).
- This will now be run automatically for every release. All processed data will be available on the nf-core website: https://nf-co.re/eager/results
- You can run this yourself using
-profile test_full
- You can run this yourself using
- This will now be run automatically for every release. All processed data will be available on the nf-core website: https://nf-co.re/eager/results
- Fixed AWS full test profile.
- #587 - Re-implemented AdapterRemovalFixPrefix for DeDup compatibility of including singletons
- #602 - Added the newly available GATK 3.5 conda package.
- #610 - Create bwa_index channel when specifying circularmapper as mapper
- Updated template to nf-core/tools 1.12.1
- General documentation improvements
- Flag
--gatk_ug_jar
has now been removed as GATK 3.5 is now avaliable within the nf-core/eager software environment.
- #591 - Fixed offset underlines in lane merging diagram in docs
- #592 - Fixed issue where supplying Bowtie2 index reported missing bwamem_index error
- #590 - Removed redundant dockstore.yml from root
- #596 - Add workaround for issue regarding gzipped FASTAs and pre-built indices
- #589 - Updated template to nf-core/tools 1.11
- #582 - Clarify memory limit issue on FAQ
- Major Automated cloud tests with large-scale data on AWS
- Major Re-wrote input logic to accept a TSV 'map' file in addition to direct paths to FASTQ files
- Major Added JSON Schema, enabling web GUI for configuration of pipeline available here
- Major Lane and library merging implemented
- When using TSV input, one library with the multiple lanes will be merged together, before mapping
- Strip FASTQ will also produce a lane merged 'raw' but 'stripped' FASTQ file
- When using TSV input, one sample with multiple (same treatment) libraries will be merged together
- Important: direct FASTQ paths will not have this functionality. TSV is required.
- #40 - Added the pileupCaller genotyper from sequenceTools
- Added validation check and clearer error message when
--fasta_index
is provided and filepath does not end in.fai
. - Improved error messages
- Added ability for automated emails using
mailutils
to also send MultiQC reports - General documentation additions, cleaning, and updated figures with CC-BY license
- Added large 'full size' dataset test-profiles for ancient fish and human contexts human
- #257 - Added the bowtie2 aligner as option for mapping, following Poullet and Orlando 2020 doi: 10.3389/fevo.2020.00105
- #451 - Adds ANGSD genotype likelihood calculations as an alternative to typical 'genotypers'
- #566 - Add tutorials on how to set up nf-core/eager for different contexts
- Nuclear contamination results are now shown in the MultiQC report
- Tutorial on how to use profiles for reproducible science (i.e. parameter sharing between different groups)
- #522 - Added post-mapping length filter to assist in more realistic endogenous DNA calculations
- #512 - Added flexible trimming of BAMs by library type. 'half' and 'none' UDG libraries can now be trimmed differentially within a single eager run.
- Added a
.dockstore.yml
config file for automatic workflow registration with dockstore.org - Updated template to nf-core/tools 1.10.2
- #544 - Add script to perform bam filtering on fragment length
- #456 - Bumps the base (default) runtime of all processes to 4 hours, and set shorter time limits for test profiles (1 hour)
- #552 - Adds optional creation of MALT SAM files alongside RMA6 files
- Added eigenstrat snp coverage statistics to MultiQC report. Process results are published in
genotyping/*_eigenstrat_coverage.txt
.
- #368 - Fixed the profile
test
to contain a parameter for--paired_end
- Mini bugfix for typo in line 1260+1261
- #374 - Fixed output documentation rendering not containing images
- #379 - Fixed insufficient memory requirements for FASTQC edge case
- #390 - Renamed clipped/merged output directory to be more descriptive
- #398 - Stopped incompatible FASTA indexes being accepted
- #400 - Set correct recommended bwa mapping parameters from Schubert et al. 2012
- #410 - Fixed nf-core/configs not being loaded properly
- #473 - Fixed bug in sexdet_process on AWS
- #444 - Provide option for preserving realigned bam + index
- Fixed deduplication output logic. Will now pass along only the post-rmdup bams if duplicate removal is not skipped, instead of both the post-rmdup and pre-rmdup bams
- #497 - Simplifies number of parameters required to run bam filtering
- #501 - Adds additional validation checks for MALT/MaltExtract database input files
- #508 - Made Markduplicates default dedupper due to narrower context specificity of dedup
- #516 - Made bedtools not report out of memory exit code when warning of inconsistent FASTA/Bed entry names
- #504 - Removed uninformative sexdeterrmine-snps plot from MultiQC report.
- Nuclear contamination is now reported with the correct library names.
- #531 - Renamed 'FASTQ stripping' to 'host removal'
- Merged all tutorials and FAQs into
usage.md
for display on nf-co.re - Corrected header of nuclear contamination table (
nuclear_contamination.txt
). - Fixed a bug with
nSNPs
definition inprint_x_contamination.py
. Number of SNPs now correctly reported print_x_contamination.py
now correctly converts all NA values to "N/A"- Increased amount of memory MultiQC by default uses, to account for very large nf-core/eager runs (e.g. >1000 samples)
- Added sequenceTools (1.4.0.6) that adds the ability to do genotyping with the 'pileupCaller'
- Latest version of DeDup (0.12.6) which now reports mapped reads after deduplication
- #560 Latest version of Dedup (0.12.7), which now correctly reports deduplication statistics based on calculations of mapped reads only (prior denominator was total reads of BAM file)
- Latest version of ANGSD (0.933) which doesn't seg fault when running contamination on BAMs with insufficient reads
- Latest version of MultiQC (1.9) with support for lots of extra tools in the pipeline (MALT, SexDetERRmine, DamageProfiler, MultiVCFAnalyzer)
- Latest versions of Pygments (7.1), Pymdown-Extensions (2.6.1) and Markdown (3.2.2) for documentation output
- Latest version of Picard (2.22.9)
- Latest version of GATK4 (4.1.7.0)
- Latest version of sequenceTools (1.4.0.6)
- Latest version of fastP (0.20.1)
- Latest version of Kraken2 (2.0.9beta)
- Latest version of FreeBayes (1.3.2)
- Latest version of xopen (0.9.0)
- Added Bowtie 2 (2.4.1)
- Latest version of Sex.DetERRmine (1.1.2)
- Latest version of endorS.py (0.4)
- 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 merged reads 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 consensus 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
- #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 any more
- #220 - Added post-mapping filtering statistics module and corresponding MultiQC statistics #217
- #152 - DamageProfiler errors won't crash entire pipeline any more
- #176 - Increase runtime for DamageProfiler on large reference genomes
- #172 - DamageProfiler errors won't crash entire pipeline any more
- #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 calmd
generated files by running throughsa]mtools view
first - #221 - Fix BWA Index not being reused by multiple samples
- 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
- #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
- #151 - Fixed post-deduplication step errors
- #147 - Fix Samtools Index for large references
- #145 - Added Picard Memory Handling fix
- Picard Tools 2.18.23 -> 2.18.27
- GATK 4.0.12.0 -> 4.1.0.0
- FastP 0.19.6 -> 0.19.7
- #127 - Added a second test case for testing the pipeline properly
- #129 - Support BAM files as input format
- #131 - Support different reference genome file extensions
- #128 - Fixed reference genome handling errors
- Picard Tools 2.18.21 -> 2.18.23
- R-Markdown 1.10 -> 1.11
- FastP 0.19.5 -> 0.19.6
- #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
- #115 - Add DamageProfiler MultiQC support
- #122 - Add pulling from Dockerhub again
- #110 - Fix for MultiQC Missing Second FastQC report
- #112 - Remove redundant UDG options
- #80 - BWA Index file handling
- #77 - Lots of documentation updates by @jfy133
- #81 - Renaming of certain BAM options
- #92 - Complete restructure of BAM options
- #84 - Fix for Samtools index issues
- #96 - Fix for MarkDuplicates issues found by @nilesh-tawari
- Added Slack button to repository readme
- #70 - Uninitialized
readPaths
warning removed
- #73 - Travis CI Testing of Conda Environment added
- #72 - iconv Issue with R in conda environment
- #69 - FastQC issues with conda environments
Initial release of nf-core/eager:
- 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.