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nf-core/raredisease: Changelog

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

v1.2.0 - Genie [xxxx-xx-xx]

Added

  • Use nf-validation plugin for parameter and samplesheet validation #386

Changed

  • Tiddit updated to v3.6.1 #385
  • Installed the nf-core version of the sentieon/bwamemindex module #397
  • Installed the nf-core version of the sentieon/bwamem module #398
  • Installed the nf-core version of the sentieon/readwriter module #399
  • Installed the nf-core version of the sentieon/datametrics module #400
  • Installed the nf-core version of the sentieon/dedup module. The dedup module also contains a call to Sentieon's LocusCollector #401
  • Removing Sentieon-based BQSR. Recent Illumina sequencers tend to provide well-calibrated BQs, so BQSR may not provide much benefit #402
  • Installed the nf-core version of the sentieon/dnamodelapply module #403
  • Installed the nf-core version of the sentieon/wgsmetricsalgo module #404
  • Installed the nf-core version of the sentieon/dnascope module #406

Fixed

  • Invalid GATK4 container which caused incorrect singularity downloads with nf-core download nf-core/modules #3668
  • Make the default cram prefix same as markduplicates prefix #392
  • Sort ranked SV vcf before indexing with tabix #393
  • Make target bed file optional for WGS mode (Issue #375) #395
  • Added constraints to block the pipeline from running CollectWgsMetrics on WES samples #396

v1.1.1 - Abu (Patch) [2023-07-26]

Fixed

  • Avoids errors thrown by bcftools concat due to sample names in input vcf files not being in same order #388

v1.1.0 - Abu [2023-07-21]

Added

  • Add GATK's cnv calling pipeline #362
  • GATK's ShiftFasta to generate all the files required for mitochondrial analysis #354
  • Feature to calculate CADD scores for indels #325
  • HmtNote to annotate mitochondria #355
  • MT del script to detect mitochondrial deletions #349
  • eKLIPse to identify large mitochondrial deletions #365
  • UPD+Chromograph to identify and visualize UPD sites and regions in the chromosomes #364 and #366
  • Added check for presence of case id for each sample in samplesheet #357

Fixed

  • Avoiding publishing uncompressed VCF-file from HMTNOTE_ANNOTATE. (The corresponding compressed VCF-file still gets published.) #368

v1.0.0 - Aladdin [2023-06-01]

Initial release of nf-core/raredisease, created with the nf-core template.

Added

  • FastQC read quality control
  • Read mapping with BWAmem2/Sentieon
  • Qualimap & Picard tools quality control metrics
  • Call repeat expansions with ExpansionHunter and Stranger
  • SNV calling with DeepVariant/Sentieon
  • SV calling with Manta and TIDDIT
  • SNV annotation with bcftools roh, vcfanno, and vep
  • SV annotation with SVDB query and vep
  • Separate workflow for analysing and annotating mitochondrial variants
  • Call copy number variants in the SMN gene using SMNCopyNumberCaller