v1.6.0

Changed

• VCFs generated by the --snp option are now automatically annotated with SnpEff, incorporating ClinVar annotations
  • This can be switched off with --skip_annotation
• Bumped minimum required Nextflow version to 22.10.8
• Updated wf-basecalling subworkflow to 0.7.1 (Dorado 0.3.0)
• Enum choices are enumerated in the --help output
• Enum choices are enumerated as part of the error message when a user has selected an invalid choice
• Made it easier to see which basecaller configurations can be used for basecalling and which configurations are presented to allow small variant calling of existing datasets
  • Basecaller configurations prefixed with clair3: cannot be used for basecalling

Added

• v4.2.0 basecalling models, which must be used for sequencing runs performed at new 5 kHz sampling rate
• v4.1.0 basecalling models replace v4.0.0 models and must be used for sequencing runs performed at 4 kHz sampling rate
• Clair3 260bps models

Fixed

• Workflow get_filter_calls_command crashes with stranded interval BED
• CRAM inputs are now converted internally to BAM to avoid CNV subworkflow crash
• Basecalls and alignments are emitted in BAM to support CNV subworkflow if selected
• Workflow incorrectly prompting for an --old_ref when providing unaligned CRAM

v1.5.2

Added

• Configuration for running demo data in AWS

Changed

• Reports for wf-human-sv and wf-human-snp

Fixed

• Coverage plot not working when a bed region file is provided
• Workflow crashing with --bam_min_coverage 0
• Subworkflows that require hg19/GRCh37 now correctly accept references where chromosome sequence names do not have the 'chr' prefix

v1.5.1

Changed

• Depth of sequencing plots moved to alignment report

Fixed

• Corrected bin size unit displayed on CNV report

v1.5.0

Added

• Workflow outputs alignment statistics report when alignment has been performed

Changed

• Updated Clair3 to v1.0.1 to bump WhatsHap dependency to v1.7
• Bumped base container to use samtools 1.17 to prevent user reported segfault during minimap2_ubam process

v1.4.0

Added

• --depth_intervals will output a bedGraph file with entries for each genomic interval featuring homogeneous depth
• --phase_methyl will output haplotype-level methylation calls, using the HP tags added by whatshap in the wf-human-snp workflow
• --sv_benchmark will benchmark SV calls with Truvari
  • The workflow uses the 'NIST_SVs_Integration_v0.6' truth set and benchmarking should be carried out on HG002 data.

Changed

• Added coverage barrier to wf-human-variation
• When the SNP and SV subworkflows are both selected, the workflow will use the results of the SV subworkflow to refine the SNP calls
  • This new behaviour can be disabled with --skip_refine_snp_with_sv
• Updated to Oxford Nanopore Technologies PLC. Public License
• Workflow requires target regions to have 20x mean coverage to permit analysis

Fixed

• report_sv.py now handles empty VCF files
• report_str.py now handles mono-allelic STR
• WhatsHap processes do not block for long time with CRAM inputs due to missing REF_PATH
• filterCalls failure when input BED has more than three columns
• get_genome assumed STR subworkflow was always enabled, preventing CNV analysis with hg19
• "genome build (...) is not compatible with this workflow" was incorrectly thrown when the workflow stopped before calling get_genome

v1.3.0

Added

• --str enables STR genotyping using Straglr (compatible with genome build 38 only)

Changed

• Minor performance improvement when checking for empty VCF in aggregate pileup steps

v1.2.0

Added

• --cnv enables CNV calling using QDNAseq

v1.1.0

Changed

• Updated Dorado container image to use Dorado v0.1.1
  • Latest models are now v4.0.0
  • Workflow prints a more helpful error when Dorado fails due to unknown model name
• Updated wf-human-snp container image to load new Clair3 models for v4 basecalling
• Default basecaller_cfg set to [email protected]

Added

• --basecaller_args may be used to provide custom arguments to the basecalling process

v1.0.1

Changed

• Default basecaller_cfg set to [email protected]
• Updated description in manifest

v1.0.0

Added

• nextflow run epi2me-labs/wf-human-variation --version will now print the workflow version number and exit

Changed

• --modbam2bed_args can be used to further configure the wf-methylation modbam2bed process
• modbam2bed outputs are now prefixed with <sample_name>.methyl
• --basecall_cfg is now required by the SNP calling subworkflow to automatically pick a suitable Clair3 model
  • Users no longer have to provide --model for the SNP calling subworkflow
• Tidied workflow parameter schema
  • Some advanced options that are primarily used for benchmarking are now hidden but can be listed with --help --show_hidden_params
• wf-basecalling subworkflow now separates reads into pass and fail CRAMs based on mean qscore
  • The workflow will index and align both the pass and fail reads and provide a CRAM for each in the output directory
  • Only pass reads are used for downstream variant calling
• Updated wf-human-variation-snp container to use Sniffles v2.0.7

Removed

• -profile conda is no longer supported, users should use -profile standard (Docker) or -profile singularity instead
• --report_name is no longer required and reports will be prefixed with --sample_name instead

Fixed

• Workflow will exit with "No files match pattern" if no suitable files are found to basecall
  • Ensure to set --dorado_ext to fast5 or pod5 as appropriate