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Releases: nf-core/eager

[2.5.2] - Bopfingen (Patch) - 2024-06-28

28 Jun 12:14
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[2.5.2] - 2024-06-28

Added

  • #1079 - Added the lanemerging output directory in the output documentation (♥ to @TessaZei for reporting, fix by @TCLamnidis).

Fixed

Dependencies

Deprecated

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

21 Feb 11:12
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[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

07 Nov 12:46
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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

16 May 17:16
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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

17 Nov 10:00
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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

02 Aug 13:38
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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

08 Apr 19:18
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[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

24 Mar 14:58
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[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

24 Jan 17:02
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[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

30 Nov 13:57
20b0be4
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[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