Ecosyste.ms: Issues

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GitHub / nf-core/sarek issues and pull requests

#495 - [FEATURE] Tumor mutational burden (TMB) scoring

Issue - State: open - Opened by apeltzer over 2 years ago - 17 comments
Labels: enhancement

#492 - Housekeeping

Pull Request - State: closed - Opened by FriederikeHanssen over 2 years ago - 1 comment

#479 - Add subworkflows

Pull Request - State: closed - Opened by FriederikeHanssen over 2 years ago - 10 comments

#478 - Replace nfcore modules

Pull Request - State: closed - Opened by FriederikeHanssen almost 3 years ago - 1 comment

#477 - Replace modules with nf-core/modules

Pull Request - State: closed - Opened by FriederikeHanssen almost 3 years ago - 1 comment

#476 - add umi subworkflow

Pull Request - State: closed - Opened by FriederikeHanssen almost 3 years ago

#462 - nf-core modules update all with prefix annotation

Pull Request - State: closed - Opened by FriederikeHanssen almost 3 years ago - 3 comments

#458 - [BUG] Root filesystem extraction failed, during BaseRecalibrator step

Issue - State: closed - Opened by jowkar almost 3 years ago - 1 comment
Labels: bug, moreinfo

#438 - [BUG] BaseRecalibrator terminated

Issue - State: closed - Opened by olanio almost 3 years ago
Labels: bug, moreinfo

#430 - [BUG] BaseRecalibrator errors

Issue - State: closed - Opened by jacorvar about 3 years ago - 9 comments
Labels: bug, moreinfo

#428 - [BUG] Control-FREEC 'Stack Smashing' error with Mouse SNP file

Issue - State: closed - Opened by MikeWLloyd about 3 years ago - 5 comments
Labels: bug

#407 - GA4GH compliant

Issue - State: open - Opened by FriederikeHanssen about 3 years ago - 1 comment
Labels: enhancement, help wanted, question

#405 - Create a sentieon specific subworkflow for DSL2

Issue - State: open - Opened by maxulysse about 3 years ago - 8 comments
Labels: sentieon

#395 - adaptation for custom read names (specifically MGISEQ)

Issue - State: closed - Opened by raimondsre about 3 years ago - 4 comments
Labels: enhancement, question

#391 - [BUG] Sentieon_BQSR is not skipped when dbsnp and indel files are not provided

Issue - State: closed - Opened by grendon over 3 years ago - 3 comments
Labels: bug, sentieon

#388 - Add cram support + read splitting with seqkit for speedup

Pull Request - State: closed - Opened by FriederikeHanssen over 3 years ago - 5 comments

#321 - Sarek should have an error or at least a warning when no fasta params

Issue - State: closed - Opened by pablosoro over 3 years ago - 3 comments
Labels: bug, input validation

#320 - Set MarkDuplicates Max_Records_in_RAM to default value

Pull Request - State: closed - Opened by FriederikeHanssen over 3 years ago

#298 - Add SplitFastq module

Pull Request - State: closed - Opened by FriederikeHanssen almost 4 years ago

#226 - Look into GATK Best Practices Pipeline for $5 per genome

Issue - State: open - Opened by maxulysse over 4 years ago
Labels: enhancement

#100 - Provide reference files for WES for ASCAT

Issue - State: open - Opened by maxulysse over 4 years ago - 5 comments
Labels: enhancement

#95 - Community feedback needed: Consider other tools

Issue - State: open - Opened by maxulysse over 4 years ago - 24 comments
Labels: enhancement, community-feedback