0.3.2

Fixed

Fixed the release test profile not working after updates to testdata (#395)

Full Changelog: 0.3.1...0.3.2

0.3.1

Fixed

Fixed single sample SNV VCFs containing variants from all samples, resulting in a large number of empty GT calls (#357)

Full Changelog: 0.3.0...0.3.1

0.3.0

Highlights

• Added initial nf-test to pipeline and subworkflows
• Added test profile and CNV-calling for ONT-data
• Added repeat expansion annotation with stranger
• Added additional annotation of SNVs and INDELs, including CADD-scores for INDELs
• Added ranking of SNVs and INDELs with genmod
• Added citations, references and additional tools to the MultiQC report
• Updated DeepVariant to 1.6.1 for improved haploid variant calling
• Updated output file organisation
• Updated and improved usage and output documentation
• BAM files are now treated as the primary input file type, improving processing time
• Fixed tags in input BAM files being transfered over to (re)aligned BAM (#231)
• Fixed duplicate SNVs in outputs when providing a BED-file with overlapping regions (#252)

Known issues

• Genmod assigns wrong model types on chrX

Full Changelog: 0.2.0...0.3.0

0.2.0

What's changed

• Added somalier to automatically infer and update the sex of samples with unknown sex, and paraphase to call paralogous genes
• Added the ability to use multiple input files per sample
• Updated output files and directories
• Updated usage and output documentation
• Updated software versions for samtools to 1.20, bcftools to 1.20, gfastats to 1.3.6, mosdepth to 0.3.8, bgzip to 1.19.1, tabix to 1.19.1, minimap2 to 2.28, hifiasm to 0.19.8 and modkit to 0.3.0
• Fixed missing software versions in reports
• Fixed a nondescriptive error when no --vep_cache was supplied

Full Changelog: 0.1.0...0.2.0

0.1.0

Initial release of genomic-medicine-sweden/nallo, created with the nf-core template.

Note that this pipeline is still in its initial development stage. If you encounter any bugs or have suggestions, please open an issue.