Terrible Tiger

• Add fix for sample replicates with different split sizes
• Add option to use samtools for duplicate marking
• Updated modules
• Updated to nf-core template v2.8
• Fix issue where unaligned samples were not merged and fixed naming
• Add minimal support for sample "tags" in sample sheet
• Add panel coverage analysis
• Limit panel coverage analyses to samples with WES/WGS tags
• Make BAM_ARCHIVE accept channels with cram files
• Drop ELPREP support
• Add support for cram and index outputs in SAMTOOLS_SORMADUP
• Add option to disable marking duplicates
• Update to nf-core template v2.9
• Start using nf-validation for input parsing
• Drop support for generating aligner indices

What's Changed

• re-add metro map by @nvnieuwk in #52
• bump modules by @matthdsm in #53
• Fix/unbalanced chunks by @matthdsm in #55
• add samtools markdup by @matthdsm in #56
• bump modules by @matthdsm in #57
• Template merge by @matthdsm in #58
• fix unaliged issue, fixed #60 by @matthdsm in #63
• Feat/expand coverage by @matthdsm in #65
• Template merge by @matthdsm in #69
• Fix typo in nextflow.config by @nvnieuwk in #70
• Nf validation by @matthdsm in #71
• Template merge by @matthdsm in #72
• Cleanup by @matthdsm in #73
• Update all modules to the latest version by @nvnieuwk in #75
• Release PR by @matthdsm in #59

New Contributors

• @nvnieuwk made their first contribution in #52

Full Changelog: v1.1.2...v1.2.0