Published July 21, 2022
| Version 3.0
Software
Open
nf-core/sarek: Sarek 3.0 - Skierfe
Creators
- Maxime U. Garcia1
- FriederikeHanssen2
- Gisela Gabernet3
- WackerO
- SusiJo
- Chela James
- Anders Sune Pedersen
- Alexander Peltzer4
- José Fernández Navarro
- nickhsmith
- Edmund Miller
- David Mas-Ponte5
- nf-core bot
- Malin Larsson6
- Szilveszter Juhos7
- Abhinav Sharma8
- Adrian Lärkeryd9
- Francesco Lescai
- Lasse Folkersen10
- Lucia Conde11
- Bruno Grande12
- Paul Cantalupo
- Pablo Riesgo-Ferreiro13
- Phil Ewels14
- Sabrina Krakau3
- arontommi
- GCJMackenzie
- Johannes Alneberg15
- Olga Botvinnik16
- Kevin Menden2
- 1. @SciLifeLab | Karolinska Institutet
- 2. QBiC
- 3. @qbicsoftware
- 4. Boehringer Ingelheim
- 5. @GenomeDataScience
- 6. SciLifeLab
- 7. Morgan Stanley Budapest
- 8. @seqeralabs @biosharp-dotnet
- 9. ICR
- 10. NucleusGenomics | mynucleus.com
- 11. University College London
- 12. @Sage-Bionetworks
- 13. @TRON-Bioinformatics
- 14. Seqera Labs
- 15. National Genomics Infrastructure
- 16. @czbiohub
Description
- Porting to DSL2
- Use CRAM files where possible
- Add new tools: DragMap, DeepVariant, Joint germline calling, Haplotypecaller single sample, CNVKit Somatic, Tiddit Somatic
- Replaced tools: Trimgalore -> Fastp, Qualimap -> Mosdepth
- New references: BWAMem2, DragMap, Germline Resource
- Add a new entry
--step markduplicates - Steps can be started from bam or cram files
- Added
--paired_variant_calling_onlyto skip normal computations for paired samples - Only unmatched tumor samples will be run in single mode
- Input fastq files are split by default and mapped in parallel
- Bam2Fastq: changed to using samtools
- Samplesheet is now in CSV format with a header line with improved validation and flexibility
- New parameter
--skip_toolsretires--skip_qc,--skip_markduplicatesand--skip_bqsr --sequencing_centerrenamed to --seq_platform`- New parameter
--wesmust be set for targeted data - New parameter
--save_bam_ouputto store results file in BAM format instead of CRAM - Additional VEP output formats
- Additional VEP plugins: loftee, spliceAI, spliceRegions, dbnsfp
- Remove sentieon support
- @abhi18av made their first contribution in https://github.com/nf-core/sarek/pull/394
- @nickhsmith made their first contribution in https://github.com/nf-core/sarek/pull/454
- @Emiller88 made their first contribution in https://github.com/nf-core/sarek/pull/465
- @priesgo made their first contribution in https://github.com/nf-core/sarek/pull/432
- @SusiJo made their first contribution in https://github.com/nf-core/sarek/pull/545
- @asp8200 made their first contribution in https://github.com/nf-core/sarek/pull/571
- @lassefolkersen made their first contribution in https://github.com/nf-core/sarek/pull/591
- @WackerO made their first contribution in https://github.com/nf-core/sarek/pull/570
Full Changelog: https://github.com/nf-core/sarek/compare/2.7.2...3.0
Files
nf-core/sarek-3.0.zip
Files
(8.1 MB)
| Name | Size | Download all |
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md5:04b52302d63961166a3c0aa9cde34e12
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Additional details
Related works
- Is supplement to
- https://github.com/nf-core/sarek/tree/3.0 (URL)