Related Issues (20)
- :sparkles: accept input data as samples data file
- :wrench: add an option to export BAM files as results
- :sparkles: add a step for sample coverage
- :bug: called VCFs have unknown samples
- :arrow_up: upgrade modules to latest version HOT 1
- :zap: improve performance of coverage step
- :sparkles: support for --help command and parameters check
- :bug: check_samplesheet can't detect header in certain conditions
- :bug: solve linting issues
- :sparkles: normalize VCF file
- :arrow_up: upgrade module dependencies
- :wrench: update pipeline limits
- :zap: split chromosome relying on BAM size while running freebayes
- :zap: call freebayes in different processes
- :bug: update pipeline to support latest nf-core/tools
- :sparkles: check that reads IDs are unique
- :arrow_up: upgrade module dependencies and test for `-stub` option
- :sparkles: use MultiQC with all supported tools
- :fire: can samtools/index be removed
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