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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
AGeNT enhancement New feature or request
#1630 opened Aug 26, 2024 by RP-Bioinfo
RFE: Variant decomposition enhancement New feature or request
#1609 opened Aug 1, 2024 by lbeltrame
2
Add msisensor-pro tumor-only mode enhancement New feature or request
#1599 opened Jul 17, 2024 by bounlu
@jfnavarro
Add lofreq call-parallel (tumor-only) and lofreq somatic as variant callers enhancement New feature or request
#1588 opened Jul 11, 2024 by nevinwu
@nevinwu @AitorPeseta
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
6
Human and mouse read disambiguation for PDX samples? enhancement New feature or request
#1578 opened Jun 30, 2024 by apsteinberg
3
Test and document that Sarek can handle input-samplesheets with mixed samples docs enhancement New feature or request samplesheet
#1576 opened Jun 25, 2024 by asp8200 3.5
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
1
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
1
add nf-boost enhancement New feature or request
#1450 opened Mar 28, 2024 by maxulysse
2
meta-sarek: One pipeline to rule them all enhancement New feature or request
#1446 opened Mar 21, 2024 by matthdsm
ASCAT WES reference resources enhancement New feature or request
#1432 opened Mar 7, 2024 by wlyucl
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
2
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
sambamba/markdup enhancement New feature or request
#1367 opened Dec 28, 2023 by stavgrossfeld
@stavgrossfeld
1
NGSCHECKMATE_NCM enhancement New feature or request
#1366 opened Dec 27, 2023 by lucianhu
@SPPearce
6
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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