nf-core sarek issues - Githubissues

nf-core / sarek

Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing

https://nf-co.re/sarek

MIT License

410 stars 417 forks source link

issues

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Error with Index Out of Bounds When Running Sarek WES Pipeline with Tools Enabled (e.g., Mutect2)

#1739 kristianunger closed 1 day ago
1
Implemented TMB score calculation

#1738 bounlu opened 2 days ago
2
Implemented MSISENSORPRO tumor-only analysis

#1737 bounlu opened 2 days ago
1
How to implement sarek for plant variant calling？

#1736 meng-hhh opened 3 days ago
1
No output and no run for variant calling

#1735 dazauzai opened 3 days ago
0
Add spring and ubam files to overview pictures

#1734 FriederikeHanssen closed 4 days ago
1
Use original QC values for Deepvariant after BQSR

#1733 FriederikeHanssen opened 6 days ago
3
strange bug, two reverse conclusion are shown out at the same run

#1732 dazauzai opened 1 week ago
5
Migrate controlfreec pytest to nf-test

#1731 maxulysse opened 1 week ago
2
style: Enable harshilAlignment in VS Code workspace

#1730 edmundmiller closed 1 week ago
1
ci: Remove pytest-workflow

#1729 edmundmiller opened 1 week ago
1
Don't convert input bam files that are supplied in post-alignment steps, it's not necessary.

#1728 FriederikeHanssen closed 1 week ago
1
Tweaks to MarkDups and Bug Fix for latest version of nextflow

#1727 soccin closed 2 weeks ago
1
Error running Control-FREEC on WXS data

#1726 danro9685 opened 2 weeks ago
1
Unable to start

#1725 dbarras2 opened 2 weeks ago
5
question regarding computational power

#1724 mggrami opened 2 weeks ago
1
No such property: enable for class: java.lang.String - nextflow.enable.configProcessNamesValidation problem

#1723 allyssonallan closed 2 weeks ago
3
the vcf file from haplotypecaller was not annotated by snpeff and vep

#1722 ybdong919 opened 2 weeks ago
2
WIP Internal Benchmarking

#1721 famosab opened 2 weeks ago
6
how to use custom vep database for microbe, such as Candian.aruis

#1720 ybdong919 opened 3 weeks ago
0
Provide default UMI/trimming library specific values

#1719 maxulysse opened 3 weeks ago
0
The target server failed to respond

#1718 torres-HI opened 3 weeks ago
1
Tutorial: long reads analysis

#1717 lescai opened 3 weeks ago
0
Check if flowcell id is uniform in a fastq file

#1716 pmoris opened 3 weeks ago
0
Add library metadata and extend read group info

#1715 pmoris opened 3 weeks ago
0
Tutorial: UMI

#1714 FriederikeHanssen opened 3 weeks ago
0
Tutorial: CNV calling

#1713 FriederikeHanssen opened 3 weeks ago
0
Fix: Missing import statements on error messages(#1566)

#1712 pharmlovex closed 3 weeks ago
1
Migrate strelka pytest to nf-test

#1711 maxulysse closed 1 week ago
1
Support for PureCN

#1710 lbeltrame opened 3 weeks ago
4
Remove Strelka tumor-only somatic variant calling

#1709 nevinwu closed 3 weeks ago
4
Migrate pipeline pytest alignment and annotation tests to nf-test

#1708 maxulysse closed 3 weeks ago
1
Clean up schema file

#1707 FriederikeHanssen closed 3 weeks ago
1
Adding Variant Calling tutorial pages to Usage section

#1706 lescai closed 3 weeks ago
1
Parabricks fq2bam and applybqsr

#1705 famosab closed 3 weeks ago
1
Proposals for Sarek Tutorials on use-cases

#1704 lescai opened 3 weeks ago
3
Shard 5 : Error: no valid tests found

#1703 maxulysse opened 3 weeks ago
0
Update nf-schema tests that were not failing on lenient mode

#1702 maxulysse closed 3 weeks ago
1
Add full test report

#1701 edmundmiller opened 3 weeks ago
2
Remove pytest-workflow

#1700 edmundmiller opened 3 weeks ago
0
Get a full nf-test report in cis

#1699 edmundmiller opened 3 weeks ago
0
Fix nf-schema bug

#1698 edmundmiller closed 3 weeks ago
2
Hackathon Items

#1697 edmundmiller opened 3 weeks ago
0
transfer variant calling tutorial on nf-core/sarek repo

#1696 lescai closed 3 weeks ago
0
update all modules + fix schema_input

#1695 maxulysse closed 3 weeks ago
1
FIX: manifest DOI display on CLI

#1694 maxulysse closed 1 month ago
1
fix flowcell access

#1693 FriederikeHanssen closed 1 month ago
1
update VEP to 113.0

#1692 maxulysse closed 4 weeks ago
2
`vep_loftee` doesn't add the expected columns to `INFO/CSQ`

#1691 MahShaaban opened 1 month ago
2
Problem with intervals file

#1690 Eduardo-Auer opened 1 month ago
3