cnr-ibba / nf-resequencing-mem

Nextflow resequencing pipeline with bwa-mem and freebayes

cnr-ibba/nf-resequencing-mem Issues

:bug: markduplicates has issues with cram files
Updated 6 months ago1
:boom: add vcfallelicprimitive step
Updated 7 months ago
:zap: optimize `samtools/depth` step
Closed 9 months ago
:sparkles: Annotate VCF file with SnpEff
Closed 9 months ago
:wrench: configure MultiQC analysis
Closed 9 months ago
:arrow_up: upgrade modules
Closed 9 months ago
:sparkles: deal with CRAM aligments
Closed 9 months ago3
:fire: can samtools/index be removed
Closed 9 months ago
:zap: Add RG in alignment step
Closed 9 months ago
:construction_worker: update CI system
Closed 9 months ago
:zap: replace `bwa` with `bwa-mem2` modules
Updated 9 months ago
:zap: replace `picard/markduplicates` with `samtools/markdup`
Updated 9 months ago
:heavy_plus_sign: switch to nf-validation plugin
Updated 9 months ago
:zap: replace `picard/markduplicates` with `sambamba/markdup`
Closed 9 months ago1
:arrow_up: upgrade module dependencies and test for `-stub` option
Closed a year ago
:sparkles: use MultiQC with all supported tools
Closed a year ago
:sparkles: check that reads IDs are unique
Closed a year ago
:bug: update pipeline to support latest nf-core/tools
Closed a year ago
:zap: call freebayes in different processes
Closed 2 years ago
:bookmark: release this pipeline to the public
Closed 2 years ago
:zap: split chromosome relying on BAM size while running freebayes
Closed 2 years ago
:sparkles: support for --help command and parameters check
Closed 2 years ago
:wrench: update pipeline limits
Closed 2 years ago
:bug: check_samplesheet can't detect header in certain conditions
Closed 2 years ago
:sparkles: normalize VCF file
Closed 2 years ago
:bug: solve linting issues
Closed 2 years ago
:arrow_up: upgrade module dependencies
Closed 2 years ago
:zap: improve performance of coverage step
Closed 2 years ago
:boom: launch freebayes on all samples
Closed 2 years ago
:sparkles: deal with compressed genomes
Closed 2 years ago
:sparkles: add a step for sample coverage
Closed 2 years ago
:sparkles: accept input data as samples data file
Closed 2 years ago
:wrench: configure local resources like current nextflow pipelines
Closed 2 years ago
:wrench: add an option to export BAM files as results
Closed 2 years ago
:bug: called VCFs have unknown samples
Closed 2 years ago
:arrow_up: upgrade modules to latest version
Closed 2 years ago1
:arrow_up: upgrade pipeline modules
Closed 2 years ago1
:boom: restructure pipeline using the new template
Closed 3 years ago
:sparkles: Test in AWS environment
Closed 3 years ago
Test in PBS environment
Closed 4 years ago1
Add missing steps to resequencing-mem pipeline
Closed 4 years ago