[2.5.1] - Bopfingen (Patch) - 2024-02-21

[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

[2.5.0] - Bopfingen - 2023-11-07

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

[2.4.7] - Wangen (Patch) - 2023-05-16

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

[2.4.6] - Wangen (Patch) - 2022-11-14

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

[2.4.5] - Wangen (Patch) - 2022-08-02

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] - Wangen (Patch) - 2022-04-08

[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] - Wangen (Patch) - 2022-03-24

[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] - Wangen (Patch, Broken Leg Edition) - 2022-01-24

[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] - Wangen (Patch) - 2021-11-30

[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

[2.4.0] - Wangen - 2021-09-14

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