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nf-core/raredisease: Changelog

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

2.2.0 - Dogmatix [2024-09-13]

Added

  • A new parameter mt_aligner to control which aligner is used to align reads to mitochondria #600
  • A new parameter par_bed to pass a PAR bed files to deepvariant #598
  • A new functionality to pass gzipped resources to vcfanno_extra_resources #589
  • A new parameter vcfanno_extra_resources to pass an extra resource to vcfanno #588
  • A new parameter scatter_count to control how many interval files are created from a genome (used to parallelize annotations) #585
  • Print warning messages if user intends to perform ranking when there are no affected samples #579
  • Two new parameters skip_repeat_annotation and skip_repeat_calling to skip calling and annotation of repeat expansions #574
  • A new parameter skip_smncopynumbercaller to skip smncopynumbercaller module #574
  • A new parameter skip_sv_calling to skip sv calling workflow #572
  • Two new parameters skip_snv_calling and skip_repeat_analysis to skip snv calling and repeat analysis respectively #571
  • Two new parameters mbuffer_mem and samtools_sort_threads to control resources given to mbuffer and samtools sort in the bwameme module #570

Changed

  • Update default vep container from v110-v112 #609
  • Default index for vcfanno extra annotation files from tbi to csi #606
  • Updated the model for Sentieon DNAScope to v1.1 #601
  • bwameme can no longer be used to align mitochondrial reads #600
  • Males' X and Y chromosomes will be treated as haploids during variant calling by deepvariant #598
  • Acceptable type for lane field in the samplesheet from number to string #597
  • Allow 0 as a valid value for sex in the samplesheet #595
  • Updated deepvariant to version 1.6.1 #587
  • Parallelized vcfanno #585
  • Skip ROH calling with bcftools if there are no affected samples #579
  • Refactored tool citation list #577
  • Removed skip_repeat_analysis added in #571 #574
  • Remove several skip parameters that had been included in the pipeline to avoid failed CI tests (see parameters table below) #574
  • readcount_intervals parameter is now mandatory for running germlinecnvcaller. #570
  • Turn off CNVnator, TIDDIT, SMNCopyNumberCaller, Gens, and Vcf2cytosure for targeted analysis #573

Fixed

  • Issues that cropped up when aligner and mt_aligner were different #605
  • Update docs to show 'vep_plugin_files' as a mandatory parameter for SNV annotation #594
  • Error in SVDB merge when only a single SV caller is run #586
  • Errors due to misplaced version statements #578
  • Stub crashes due to peddy reported in #566 [#576](https://github.com/nf-core/raredisease/pull/576]
  • Docker manifest error from gnu-wget container #570
  • Citations for bwameme #563

Parameters

Old parameter New parameter
mbuffer_mem
mt_aligner
samtools_sort_threads
skip_repeat_calling
skip_snv_calling
skip_sv_calling
skip_eklipse
skip_fastqc
skip_haplocheck
skip_qualimap
skip_smncopynumbercaller
skip_repeat_annotation
scatter_count
vcfanno_extra_resources

Tool updates

Tool Old version New version
Deepvariant 1.5.0 1.6.1
ensemblvep 110 112

2.1.0 - Obelix [2024-05-29]

Added

  • A new aligner, bwameme #553
  • A new parameter run_mt_for_wes to turn on mitochondrial analysis for targeted analysis #552
  • A new parameter bwa_as_fallback to switch aligner to bwa in case bwamem2 fails #551
  • A new parameter skip_me_calling to skip mobile element calling and the subsequent annotation of them #556

Changed

  • Changed valid values for sex according to the PED file format #550
  • Refactored config files #538
  • Refactored mobile element annotation subworkflow files #538
  • Refactored to remove "a process is defined more than once" warning #557
  • Updated modules #558

Fixed

  • Include multiallelic indel sites in CADD scoring jobs #545
  • Fixed issues with samtools merge not being run on samples sequenced over multiple lanes #538
  • Fixed join issues in the mobile element calling subworkflow which occured when mobile_element_references were not provided #556

Parameters

Old parameter New parameter
bwameme
bwa_as_fallback
run_mt_for_wes
skip_me_calling

:::note Parameter has been updated if both old and new parameter information is present. Parameter has been added if just the new parameter information is present. Parameter has been removed if new parameter information isn't present. :::

Module updates

Tool Old version New version
bwa 0.7.17 0.7.18
CADD 1.6.1 1.6.post1
Sentieon 202308.01 202308.02
bwameme 1.0.6

:::note Version has been updated if both old and new version information is present. Version has been added if just the new version information is present. Version has been removed if new version information isn't present. :::

2.0.1 - Asterix (Patch) [2024-03-25]

Fixed

  • Germlinecnvcaller subworkflow uses the output channel casecalls from germlinecnvcaller module instead of calls which was invalid. #535

2.0.0 - Asterix [2024-03-18]

Added

  • Use nf-validation plugin for parameter and samplesheet validation #386
  • A new parameter skip_vep_filter to skip filtering based on vep results #416
  • A metromap representating the core parts of the pipeline #428
  • Metromap and logos for light and dark theme #432
  • New parameters to skip qualimap and eklipse (--skip_qualimap and --skip_eklipse) #436
  • Fix "there is no process matching config selector warnings" #435
  • New parameters to skip fastqc and haplocheck (--skip_fastqc and --skip_haplocheck) #438
  • CNVnator for copy number variant calling #438
  • A new parameter svdb_query_bedpedbs to provide bedpe files as databases for SVDB query #449
  • ngsbits samplegender to check sex #453
  • New workflow for generating cgh files from SV vcfs for interpretation in the CytosSure interpretation software. Turned off by default #456
  • Fastp to do adapter trimming. It can be skipped using --skip_fastp #457
  • New workflow for calling insertion of mobile elements #440
  • GATK CNVCaller uses segments instead of intervals, filters out "reference" segments between the calls, and fixes a bug with how ch_readcount_intervals was handled #472
  • bwa aligner #474
  • Add FOUND_IN tag, which mentions the variant caller that found the mutation, in the INFO column of the vcf files #471
  • A new parameter vep_plugin_files to supply files required by vep plugins #482
  • New workflow for annotating mobile elements #483
  • Added a functionality to subsample mitochondrial alignment, and a new parameter skip_mt_subsample to skip the subworkflow #508.
  • Chromograph to plot coverage across chromosomes #507
  • Added a new parameter vep_filters_scout_fmt to supply a bed-like file exported by scout to be used in filter_vep #511.
  • Added two new parameters variant_consequences_snv and variant_consequences_sv to supply variant consequence files for annotating SNVs and SVs. #509

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
  • Breaks down mitochondrial analysis workflow into smaller subworkflows that are more modular #419
  • Replaced the parameter skip_mt_analysis which was used to turn on/off the mitochondrial workflow #419
  • Adds a new parameter skip_mt_annotation which can be used to turn on/off annotation and ranking for mitochondrial SNVs #419
  • Changed the name of the parameter from skip_cnv_calling to skip_germlinecnvcaller #435
  • Check SVDB query input files for existence and correct format #476
  • Change hardcoded platform value to params.platform in align_MT.config #475
  • The split into clincial and research VCFs is now done before ranking the varaints #485
  • Installed the nf-core version of ensemblvep/vep module #482
  • The filenames of the ranked output VCF files have been changed. See output.md for more information#485
  • Patched cnvnator module so that the processes didn't have to rerun after a failed run #503.
  • Added a local module to generate bed files with variant caller names #505.

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
  • Updated modules from nf-core #412
  • If present, remove duplicate entries in probands and upd_children in the meta. #420
  • Fixes vep starting as many instances as the square of the number of scatters. #405
  • Replaced the logic where we added an arbitrary substring to keep file names unique after alignment which we then removed using a split operator, with a simple copy operation. #425
  • Preventing a crash of rhocall annotate in the case of running four individuals whereof two are affected.
  • Fixed memory qualifier in gatk4 germlinecnvcaller and postprocessgermlinecnvcalls
  • Fixed wrong process names when outputting versions in ALIGN_SENTIEON and CALL_SNV.
  • Fixed gens subworkflow #515

Parameters

Old parameter New parameter
--cnvnator_binsize
--gens_pon_female
--gens_pon_male
--min_trimmed_length
--mobile_element_references
--mobile_element_svdb_annotations
--mt_subsample_rd
--mt_subsample_seed
--ngsbits_samplegender_method
--rtg_truthvcfs
--run_rtgvcfeval
--sample_id_map
--score_config_mt
--sdf
--pcr_amplification --sentieon_dnascope_pcr_indel_model
--skip_eklipse
--skip_fastqc
--skip_fastp
--skip_gens
--skip_germlinecnvcaller
--skip_haplocheck
--skip_me_annotation
--skip_mt_annotation
--skip_mt_subsample
--skip_peddy
--skip_qualimap
--skip_vcf2cytosure
--skip_vep_filter
--svdb_query_bedpedbs
--variant_consequences_snv
--variant_consequences_sv
--vcf2cytosure_blacklist
--vep_plugin_files
--vep_filters_scout_fmt
--gens_pon
--gens_switch
--skip_cnv_calling
--skip_mt_analysis

:::note Parameter has been updated if both old and new parameter information is present. Parameter has been added if just the new parameter information is present. Parameter has been removed if new parameter information isn't present. :::

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