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Issues: nf-core/sarek
Community feedback needed: (pre)-validation at the Sarek level
#798
opened Oct 13, 2022 by
maxulysse
Open
33
Community feedback needed: Add tutorials/faqs describing diff...
#955
opened Feb 28, 2023 by
FriederikeHanssen
Open
3
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Issues list
Implementation of Indel and Multiallelic Variant Normalization in Sarek Pipeline
enhancement
New feature or request
#1666
opened Sep 27, 2024 by
Patricie34
Add pattern for all reference files
enhancement
New feature or request
#1650
opened Sep 12, 2024 by
maxulysse
Add New feature or request
msisensor-pro
tumor-only mode
enhancement
#1599
opened Jul 17, 2024 by
bounlu
Add lofreq call-parallel (tumor-only) and lofreq somatic as variant callers
enhancement
New feature or request
#1588
opened Jul 11, 2024 by
nevinwu
Add an option to optionally use the GATK VariantFiltration instead of VQSR
enhancement
New feature or request
#1586
opened Jul 9, 2024 by
cmatKhan
DeepVariant params addition request:
enhancement
New feature or request
#1583
opened Jul 8, 2024 by
poddarharsh15
Human and mouse read disambiguation for PDX samples?
enhancement
New feature or request
#1578
opened Jun 30, 2024 by
apsteinberg
Test and document that Sarek can handle input-samplesheets with mixed samples
docs
enhancement
New feature or request
samplesheet
Pooled normals for CNVkit
enhancement
New feature or request
#1562
opened Jun 12, 2024 by
HenriettaHolze
Please add VEP plugins (Conservation and Condel)
enhancement
New feature or request
#1549
opened May 30, 2024 by
andrew2k
port CREATE_INTERVALS_BED to nf-core/modules
enhancement
New feature or request
#1523
opened May 15, 2024 by
maxulysse
Copy-Number Enhancements - Ascat joint calling
enhancement
New feature or request
#1512
opened May 7, 2024 by
maxulysse
Copy-Number Enhancements - Ascat penality
enhancement
New feature or request
#1510
opened May 7, 2024 by
seedgeorge
meta-sarek: One pipeline to rule them all
enhancement
New feature or request
#1446
opened Mar 21, 2024 by
matthdsm
Allow cram in mapping step
enhancement
New feature or request
#1424
opened Feb 24, 2024 by
saulpierotti
Better error message for empty fastq files
enhancement
New feature or request
input validation
#1416
opened Feb 21, 2024 by
SpikyClip
Check and update local and nf-core modules, to make sure output does not encapsulate input
enhancement
New feature or request
#1392
opened Feb 6, 2024 by
maxulysse
7 of 98 tasks
Run BAM QC after alignment
enhancement
New feature or request
#1379
opened Jan 18, 2024 by
Matteodigg
Allow to specify a local config file for snpEff
enhancement
New feature or request
#1355
opened Dec 12, 2023 by
maxulysse
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