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nf-core/eager: Changelog

The format is based on Keep a Changelog and this project adheres to Semantic Versioning.

[2.4.0] - 20201-09-14

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

[2.3.5] - 2021-06-03

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

[2.3.4] - 2021-05-05

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

[2.3.3] - 2021-04-08

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

[2.3.2] - 2021-03-16

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

Deprecated

[2.3.1] - 2021-01-14

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

[2.3.0] - 2021-01-11 - "Aalen"

Added

  • #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.

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
  • #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

Deprecated

[2.2.2] - 2020-12-09

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.

[2.2.1] - 2020-10-20

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

[2.2.0] - Ulm - 2020-10-20

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] - 2020-03-05 - "Ravensburg"

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 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/)

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 - 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

Fixed

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

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] - 2019-01-28

Added

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] - 2019-01-09

Added

Fixed

[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

Other

  • Added Slack button to repository readme

[2.0.2] - 2018-11-03

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

Fixed

  • #69 - FastQC issues with conda environments

[2.0.0] "Kaufbeuren" - 2018-10-17

Initial release of nf-core/eager:

Added

  • 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.