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