[2.5.1] - 2024-02-21

Added

• #1037 Added an option to deactivate the -sorted option of bedtools coverage, in case the feature file is not sorted the same way as the fasta file, albeit with the caveat this will be very slow. (♥ Thanks to @IdoBar for reporting, and contributing.)

Fixed

• #1048 --vcf2genome_outfile parameter now gets prefixed by the sample_name and suffixed with .fasta (i.e. <sample_name>_<vcf2genome_outfile>.fasta). This ensures we avoid overwriting the output fasta of one sample with that of another when the option is provided. (♥ Thanks to @MeriamOs for reporting.)
• #1047 Changed the row some statistics were reported in the General Stats table. The File name collision fixed in 2.5.0 (see #1017) caused these statistics to be reported in the wrong row due to an added suffix.
• #1051 An error is now thrown if input BAM files end in .unmapped.bam, as this breaks the bam filtering process and empties the bam files in the process. (♥ Thanks to @PCQuilis for reporting.)

Dependencies

Deprecated

Added

• #1020 Added mapDamage2 as an alternative for damage calculation.

Fixed

• #1017 Fixed file name collision in niche cases with multiple libraries of multiple UDG treatments.
• #1024 multiqc_general_stats.txt is now generated even if the table is a beeswarm plot in the report.
• #655 Updated RG tags for all mappers. RG-id now includes Sample as well as Library ID. Added LB: tag with the library ID.
• #1031 Always index fasta regardless of mapper. This ensures that DamageProfiler and genotyping processes get submitted when using bowtie2 and not providing a fasta index.

Dependencies

• multiqc: 1.14 -> 1.16

Deprecated

Added

Fixed

• #983 Bump pygments version due to incompatibility with MultiQC dependencies (♥ to @MinLuke for reporting, fix by @jfy133)

Dependencies

• pygments: 2.9 -> 2.14
• multiqc: 1.13 -> 1.14

Added

• #933 Added support for customising —seq-length in mapDamage rescaling (♥ to @ashildv for requesting)

Fixed

• Changed endors.py license from GPL to MIT (♥ to @aidaanva for fixing)
• Removed erroneous R2 in single-end example in input TSV of usage docs (♥ to @aidaanva for fixing)
• #928 Fixed read group incompatibility by re-adding picard AddOrReplaceReadGroups for MultiVCFAnalyzer (♥ to @aidaanva, @meganemichel for reporting)
• Fixed edge case of DamageProfiler occasionally requiring FASTA index (♥ to @asmaa-a-abdelwahab for reporting)
• #834 Increased significance values in general stats table for Qualimap mean/median coverages (♥ to @neija2611 for reporting)
• Fixed parameter documentation for --snpcapture_bed regarding on-target SNP stats to state these stats currently not displayed in MultiQC only in the Qualimap results (♥ to @meganemichel and @TCLamnidis for reporting)
• #934 Fixed broken parameter setting in mapDamage2 rescale length (♥ to @ashildv for reporting)

Dependencies

• Updated MultiQC to official 1.13 version (rather than alpha)
• Added pinned MALT dependency to ensure working version in future versions of eager

Deprecated

Added

Fixed

• #882 Define DSL1 execution explicitly, as new versions Nextflow made DSL2 default (♥ to & fix from @Lehmann-Fabian)
• #879 Add missing threads parameter for pre-clipping FastQC for single end data that caused insufficient memory in some cases (♥ to @marcel-keller for reporting)
• #880 Fix failure of endorSpy to be cached or reexecuted on resume (♥ to @KathrinNaegele, @TCLamnidis, & @mahesh-panchal for reporting and debugging)
• #885 Specify task memory for all tools in get_software_versions to account for incompatibilty of java with some SGE clusters causing hanging of the process (♥ to @maxibor for reporting)
• #887 Clarify what is considered ‘ultra-short’ reads in the help text of clip_readlength, for when you may wish to turn of length filtering during AdapterRemoval (♥ to @TCLamnidis for reporting)
• #889 Remove/update parameters from benchmarking test profiles (♥ to @TCLamnidis for reporting)
• #895 Output documentation typo fix and added location of output docs in pipeline summary (♥ to @RodrigoBarquera for reporting)
• #897 Fix pipeline crash if no Kraken2 results generated (♥ to @alexandregilardet for reporting)
• #899 Fix pipeline crash for circulargenerator if reference file does not end in .fasta (♥ to @scarlhoff for reporting)
• Fixed some missing default values in the nextflow parameter schema JSON
• #789 Substantial speed and memory optimisation of the extract_map_reads.py script (♥ to @ivelsko for reporting, @maxibor for optimisation)
• Fix staging of input bams for genotyping_pileupcaller process. Downstream changes from changes introduced when fixing endorspy caching.
• Made slight correction on metro map diagram regarding input data to SexDeterrmine (only BAM trimming output files)

Dependencies

• Updated MultiQC to latest stable alpha version on bioconda, correcting the previously nonsensical AdapterRemoval plots (♥ to @NiemannJ for fixing in MultiQC)

Deprecated

[2.4.4] - 2022-04-08

Added

Fixed

• Fixed some auxiliary files (adapater list, snpcapture/pileupcaller/sexdeterrmine BED files, and pileupCaller SNP file, PMD reference mask) in some cases only be used against one sample (❤ to @meganemichel for reporting, fix by @jfy133)

Dependencies

Deprecated

[2.4.3] - 2022-03-24

Added

Fixed

• #828 Improved error message if required metagenomic screening parameters not set correctly
• #836 Remove deprecated parameters from test profiles
• #838 Fix —snpcapture_bed files not being picked up by Nextflow (❤ to @meganemichel for reporting)
• #843 Re-add direct piping of AdapterRemovalFixPrefix to pigz
• #844 Fixed reference masking prior to pmdtools
• #845 Updates parameter documention to specify -s preseq parameter also applies to lc_extrap
• #851 Fixes a file-name clash during additional_library_merge, post-BAM trimming of different UDG treated libraries of a sample (♥ to @alexandregilardet for reporting)
• Renamed a range of MultiQC general stats table headers to improve clarity, documentation has been updated accordingly
• #857 Corrected samtools fastq flag to retain read-pair information when converting off-target BAM files to fastq in paired-end mapping (❤ to @alexhbnr for reporting)
• #866 Fixed a typo in the indexing step of BWA mem when not-collapsing (❤ to @alexhbnr for reporting)
• Corrected tutorials to reflect updated BAM trimming flags (❤ to @marcel-keller for reporting and correcting)

Dependencies

• #829 Bumped sequencetools: 1.4.0.5 -> 1.5.2
• Bumped MultiQC: 1.11 -> 1.12 (for run-time optimisation and tool citation information)

Deprecated

[2.4.2] - 2022-01-24

Added

Fixed

• #824 Fixes large memory footprint of bedtools coverage calculation. (@TCLamnidis)
• #822 Fixed post-adapterremoval trimmed files not being lane-merged and included in downstream analyses (@meganemichel)
• Fixed a couple of software version reporting commands (@jfy133)

Dependencies

Deprecated

[2.4.1] - 2021-11-30

Added

• #805 Changes to bam_trim options to allow flexible trimming by library strandedness (in addition to UDG treatment). (@TCLamnidis)
• #808 Retain read group information across bam merges. Sample set to sample name (rather than library name) in bwa output ‘RG’ readgroup tag. (@TCLamnidis)
• Map and base quality filters prior to genotyping with pileupcaller can now be specified. (@TCLamnidis)
• #774 Added support for multi-threaded Bowtie2 build reference genome indexing (@jfy133)
• #804 Improved output documentation description to add how ‘cluster factor’ is calculated (thanks to @meganemichel)

Fixed

• #803 Fixed mistake in metro-map diagram (samtools index is now correctly samtools faidx) (@jfy133)

Dependencies

Deprecated

Added

• #317 Added bcftools stats for general genotyping statistics of VCF files
• #651 - Adds removal of adapters specified in an AdapterRemoval adapter list file
• #642 and #431 adds post-adapter removal barcode/fastq trimming
• #769 - Adds lc_extrap mode to preseq (suggested by @roberta-davidson)

Fixed

• Fixed some missing or incorrectly reported software versions
• #771 Remove legacy code
• Improved output documentation for MultiQC general stats table (thanks to @KathrinNaegele and @esalmela)
• Improved output documentation for BowTie2 (thanks to @isinaltinkaya)
• #612 Updated BAM trimming defaults to 0 to ensure no unwanted trimming when mixing half-UDG with no-UDG (thanks to @scarlhoff)
• #722 Updated BWA mapping mapping parameters to latest recommendations - primarily alnn back to 0.01 and alno to 2 as per Oliva et al. 2021 (10.1093/bib/bbab076)
• Updated workflow diagrams to reflect latest functionality
• #787 Adds memory specification flags for the GATK UnifiedGenotyper and HaplotyperCaller steps (thanks to @nylander)
• Fixed issue where MultiVCFAnalyzer would not pick up newly generated VCF files, when specifying additional VCF files.
• #790 Fixed kraken2 report file-name collision when sample names have . in them
• #792 Fixed java error messages for AdapterRemovalFixPrefix being hidden in output
• #794 Aligned default test profile with nf-core standards (test_tsv is now test)

Dependencies

• Bumped python: 3.7.3 -> 3.9.4
• Bumped markdown: 3.2.2 -> 3.3.4
• Bumped pymdown-extensions: 7.1 -> 8.2
• Bumped pyments: 2.6.1 -> 2.9.0
• Bumped adapterremoval: 2.3.1 -> 2.3.2
• Bumped picard: 2.22.9 -> 2.26.0
• Bumped samtools 1.9 -> 1.12
• Bumped angsd: 0.933 -> 0.935
• Bumped gatk4: 4.1.7.0 -> 4.2.0.0
• Bumped multiqc: 1.10.1 -> 1.11
• Bumped bedtools 2.29.2 -> 2.30.0
• Bumped libiconv: 1.15 -> 1.16
• Bumped preseq: 2.0.3 -> 3.1.2
• Bumped bamutil: 1.0.14 -> 1.0.15
• Bumped pysam: 0.15.4 -> 0.16.0
• Bumped kraken2: 2.1.1 -> 2.1.2
• Bumped pandas: 1.0.4 -> 1.2.4
• Bumped freebayes: 1.3.2 -> 1.3.5
• Bumped biopython: 1.76 -> 1.79
• Bumped xopen: 0.9.0 -> 1.1.0
• Bumped bowtie2: 2.4.2 -> 2.4.4
• Bumped mapdamage2: 2.2.0 -> 2.2.1
• Bumped bbmap: 38.87 -> 38.92
• Added bcftools: 1.12

Deprecated

Added

• #722 - Adds bwa -o flag for more flexibility in bwa parameters
• #736 - Add printing of multiqc run report location on successful completion
• New logo that is more visible when a user is using darkmode on GitHub or nf-core website!

Fixed

• #723 - Fixes empty fields in TSV resulting in uninformative error
• Updated template to nf-core/tools 1.14
• #688 - Clarified the pipeline is not just for humans and microbes, but also plants and animals, and also for modern DNA
• #751 - Added missing label to mtnucratio
• General code cleanup and standardisation of parameters with no default setting
• #750 - Fixed piped commands requesting the same number of CPUs at each command step
• #757 - Removed confusing ‘Data Type’ variable from MultiQC workflow summary (not consistent with TSV input)
• #759 - Fixed malformed software scraping regex that resulted in N/A in MultiQC report
• #761 - Fixed issues related to instability of samtools filtering related CI tests

Dependencies

Deprecated

Added

• #729 Added Bowtie2 flag --maxins for PE mapping modern DNA mapping contexts

Fixed

• Corrected explanation of the “—min_adap_overlap” parameter for AdapterRemoval in the docs
• #725 bwa_index doc update
• Re-adds gzip piping to AdapterRemovalFixPrefix to speed up process after reports of being very slow
• Updated DamageProfiler citation from bioRxiv to publication

Dependencies

• Removed pinning of tbb (upstream bug in bioconda fixed)
• Bumped pigz to 2.6 to fix rare stall bug when compressing data after AdapterRemoval
• Bumped Bowtie2 to 2.4.2 to fix issues with tbb version

Deprecated

Added

• #349 - Added option enabling platypus formatted output of pmdtools misincorporation frequencies.

Fixed

• #719 - Fix filename for bam output of mapdamage_rescaling
• #707 - Fix typo in UnifiedGenotyper IndelRealigner command
• Fixed some Java tools not following process memory specifications
• Updated template to nf-core/tools 1.13.2
• #711 - Fix conditional execution preventing multivcfanalyze to run
• #714 - Fixes bug in nuc contamination by upgrading to latest MultiQC v1.10.1 bugfix release

Dependencies

Deprecated

Added

• #687 - Adds Kraken2 unique kmer counting report
• #676 - Refactor help message / summary message formatting to automatic versions using nf-core library
• #682 - Add AdapterRemoval --qualitymax flag to allow FASTQ Phred score range max more than 41

Fixed

• #666 - Fixed input file staging for print_nuclear_contamination
• #631 - Update minimum Nextflow version to 20.07.1, due to unfortunate bug in Nextflow 20.04.1 causing eager to crash if patch pulled
• Made MultiQC crash behaviour stricter when dealing with large datasets, as reported by @ashildv
• #652 - Added note to documentation that when using --skip_collapse this will use paired-end alignment mode with mappers when using PE data
• #626 - Add additional checks to ensure pipeline will give useful error if cells of a TSV column are empty
• Added note to documentation that when using --skip_collapse this will use paired-end alignment mode with mappers when using PE data
• #673 - Fix Kraken database loading when loading from directory instead of compressed file
• #688 - Allow pipeline to complete, even if Qualimap crashes due to an empty or corrupt BAM file for one sample/library
• #683 - Sets --igenomes_ignore to true by default, as rarely used by users currently and makes resolving configs less complex
• Added exit code 140 to re-tryable exit code list to account for certain scheduler wall-time limit fails
• #672 - Removed java parameter from picard tools which could cause memory issues
• #679 - Refactor within-process bash conditions to groovy/nextflow, due to incompatibility with some servers environments
• #690 - Fixed ANGSD output mode for beagle by setting -doMajorMinor 1 as default in that case
• #693 - Fixed broken TSV input validation for the Colour Chemistry column
• #695 - Fixed incorrect -profile order in tutorials (originally written reversed due to nextflow bug)
• #653 - Fixed file collision errors with sexdeterrmine for two same-named libraries with different strandedness

Dependencies

• Bumped MultiQC to 1.10 for improved functionality
• Bumped HOPS to 0.35 for MultiQC 1.10 compatibility

Added

Fixed

• #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

Dependencies

Deprecated

Added

• Major #640 - Added a pre-metagenomic screening filtering of low-sequence complexity reads with bbduk
• Major #583 - Added mapDamage2 rescaling of BAM files to remove damage
• Updated usage (merging files) and workflow images reflecting new functionality.

Fixed

• 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
• Major #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

Dependencies

• Update: DeDup v0.12.7 to v0.12.8

Added

• 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

Fixed

• 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

Deprecated

• Flag --gatk_ug_jar has now been removed as GATK 3.5 is now avaliable within the nf-core/eager software environment.

Fixed

• #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

Added

• 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.

Fixed

• #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 in print_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)

Dependencies

• 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)

[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 - 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 calmd generated files by running through sa]mtools view first
• #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] - 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

• #151 - Fixed [post-deduplication step errors](https://github.com/nf-core/eager/issues/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] - 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

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] - 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] - 2018-11-03

Maintenance release

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

Maintenance release for 2.0.1

Fixed

• #69 - FastQC issues with conda environments

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.