Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / nf-core/sarek issues and pull requests

#973 - Add --step controlfreec back in

Issue - State: open - Opened by FriederikeHanssen over 1 year ago
Labels: enhancement

#970 - Pipeline completed with errors : ControlFREEC

Issue - State: closed - Opened by Nour-EddineS over 1 year ago - 5 comments
Labels: question

#968 - CHORE: update all modules

Pull Request - State: closed - Opened by maxulysse over 1 year ago - 7 comments

#966 - Joint Genotype Calling Recalibrated VCFs Duplicate Entries; VEP is (Intentionally) Eating Variants

Issue - State: closed - Opened by evanwu1119 over 1 year ago - 3 comments
Labels: bug, PR opened

#956 - Support for PureCN for estimating purity/ploidy

Issue - State: closed - Opened by lbeltrame over 1 year ago - 4 comments
Labels: enhancement

#955 - Community feedback needed: Add tutorials/faqs describing different usages to the website

Issue - State: open - Opened by FriederikeHanssen over 1 year ago - 3 comments
Labels: enhancement, docs, community-feedback

#952 - Parallelisation of variant call across regions causes Manta to miss some variant classes

Issue - State: closed - Opened by lhonour over 1 year ago - 1 comment
Labels: bug

#951 - CNVKIT_REFERENCE error

Issue - State: closed - Opened by paolo-kunderfranco over 1 year ago - 3 comments
Labels: bug

#950 - More check for the samplesheet

Issue - State: closed - Opened by maxulysse over 1 year ago - 4 comments
Labels: enhancement, input validation

#948 - mixing tumor-only and paired samples and having a tool that only works for paired samples causes the pipeline to fail

Issue - State: open - Opened by FriederikeHanssen over 1 year ago - 3 comments
Labels: bug, input validation, moreinfo

#944 - Add target capture performance via Picard HsMetrics module

Issue - State: open - Opened by adamrtalbot over 1 year ago - 3 comments
Labels: enhancement

#943 - Pipeline stalling

Issue - State: closed - Opened by kmarianski over 1 year ago - 19 comments
Labels: bug, question

#937 - Add a section in the FAQs about annotation cache

Issue - State: open - Opened by maxulysse over 1 year ago
Labels: docs

#934 - Perform a compatibility check between bed file specified at --targets and reference genome

Issue - State: open - Opened by GeertvanGeest over 1 year ago - 3 comments
Labels: enhancement

#930 - Add more manual tests

Pull Request - State: closed - Opened by maxulysse over 1 year ago - 2 comments

#928 - No need for BAI when using uBAM

Pull Request - State: closed - Opened by maxulysse over 1 year ago - 3 comments

#925 - AD value of Strelka vcf

Issue - State: closed - Opened by aihualin over 1 year ago - 4 comments
Labels: bug, moreinfo

#924 - CNVkit reference issue for WGS tumor-only samples

Issue - State: open - Opened by berguner over 1 year ago - 16 comments
Labels: bug

#923 - joint genotyping optimal strategy

Issue - State: open - Opened by TonyKess over 1 year ago - 1 comment
Labels: help wanted

#922 - Port local sarek subworkflows to modules

Issue - State: open - Opened by maxulysse over 1 year ago
Labels: enhancement

#921 - Control-FREEC *.png output files don't show text

Issue - State: open - Opened by mauro-saporita over 1 year ago - 6 comments
Labels: bug, help wanted

#920 - Workflow execution completed unsuccessfully! due to CNVkit error

Issue - State: closed - Opened by Ahas4 over 1 year ago - 3 comments
Labels: bug

#918 - joint germline vcftools error

Issue - State: open - Opened by TonyKess over 1 year ago - 7 comments
Labels: bug

#916 - Mutect2 multi-sample mode

Issue - State: closed - Opened by berguner over 1 year ago - 1 comment
Labels: enhancement

#914 - targeted sequencing data, point mutations

Issue - State: closed - Opened by aihualin over 1 year ago - 7 comments
Labels: question, docs

#908 - Add option for outputting gvcfs instead of vcfs

Issue - State: open - Opened by asp8200 over 1 year ago - 8 comments
Labels: enhancement

#902 - Reference Allele Error on dbSNP on step HaplotypeCaller CNN1

Issue - State: open - Opened by barslmn almost 2 years ago - 1 comment
Labels: docs

#901 - configManta.py ignores `crai` index file path

Issue - State: closed - Opened by Hoeze almost 2 years ago - 1 comment
Labels: bug, moreinfo

#900 - tabix fails for large chromosome sizes

Issue - State: open - Opened by seb-mueller almost 2 years ago
Labels: bug, enhancement

#899 - CalculateContamination table needs to be sorted

Issue - State: open - Opened by wt12318 almost 2 years ago - 15 comments

#895 - add even more samplesheet checks

Issue - State: closed - Opened by maxulysse almost 2 years ago - 1 comment
Labels: enhancement, input validation

#885 - Replace the locale module add_info_to_vcf with bcftools

Issue - State: open - Opened by asp8200 almost 2 years ago
Labels: enhancement

#883 - Mention the option --concatenate_vcfs in usage.md and output.md

Issue - State: closed - Opened by asp8200 almost 2 years ago
Labels: enhancement, docs, Sarek v3.2

#882 - remove exit strategy for MANTA/STRELKA

Pull Request - State: closed - Opened by maxulysse almost 2 years ago - 5 comments

#868 - Population calling | joint calling | ensemble calling

Issue - State: open - Opened by amizeranschi almost 2 years ago - 2 comments
Labels: enhancement

#863 - Improve CNVKit

Issue - State: open - Opened by FriederikeHanssen almost 2 years ago - 3 comments
Labels: enhancement

#853 - GroupKey Logic for multiple lanes with different sizes based on line splitting

Issue - State: closed - Opened by achristofferson-bbi almost 2 years ago - 5 comments
Labels: bug

#852 - add more info about which process are affected by --wes

Issue - State: open - Opened by maxulysse almost 2 years ago
Labels: enhancement, docs

#848 - Provide typical usage of --tools

Issue - State: open - Opened by ameynert almost 2 years ago - 7 comments
Labels: enhancement

#838 - Add samtools markdup as duplicate marking alternative

Issue - State: open - Opened by FriederikeHanssen almost 2 years ago - 2 comments
Labels: enhancement

#835 - vcf-file from mpileup is not getting annotated

Issue - State: closed - Opened by asp8200 almost 2 years ago - 4 comments
Labels: enhancement, help wanted

#830 - Customize Preprocessing based on each tool

Issue - State: open - Opened by berguner almost 2 years ago - 4 comments
Labels: enhancement

#826 - BCFTools use region/target file

Issue - State: open - Opened by FriederikeHanssen almost 2 years ago
Labels: enhancement

#808 - controlfreec with multiple ploidy values results in plotting error

Issue - State: open - Opened by mjakobs almost 2 years ago - 1 comment
Labels: bug, input validation

#805 - Avoid use of exit-statements

Issue - State: closed - Opened by asp8200 almost 2 years ago - 1 comment
Labels: enhancement, input validation

#803 - Can be tumor-only somatic variant calling performed using Strelka?

Issue - State: open - Opened by ariadnaaterrades almost 2 years ago - 4 comments
Labels: bug, docs

#802 - MarkDuplicates step fails with UMIs from read names and 4 lanes

Issue - State: open - Opened by sci-kai almost 2 years ago - 9 comments
Labels: bug

#800 - segmentation fles are empty

Issue - State: closed - Opened by paumarc almost 2 years ago - 2 comments
Labels: bug

#787 - How to prepare the basic referece, GATK bundle and annotation database with bad network connection?

Issue - State: closed - Opened by xflicsu almost 2 years ago - 1 comment
Labels: bug

#778 - save_bam_mapped + gatk_spark fails

Issue - State: open - Opened by FriederikeHanssen almost 2 years ago - 1 comment
Labels: bug, good first issue, docs

#776 - replace .collect().ifEmpty([]) by .toList()

Pull Request - State: closed - Opened by maxulysse almost 2 years ago - 4 comments

#769 - containers missing in nf-core download

Issue - State: closed - Opened by egenomics about 2 years ago - 28 comments
Labels: bug

#764 - [FEATURE] Option to output gvcf files from haplotypecaller

Issue - State: closed - Opened by wpoehlm about 2 years ago - 1 comment
Labels: enhancement

#763 - Pipeline does not complete variant calling when staring from the '--step prepare_recalibration'

Issue - State: closed - Opened by senzhaocode about 2 years ago - 9 comments
Labels: bug

#755 - start pipeline from --joint_germline step

Issue - State: open - Opened by jrhaas about 2 years ago - 5 comments
Labels: enhancement

#754 - Tools load into a cluster job

Issue - State: closed - Opened by JaumeBagueCompanys about 2 years ago - 10 comments
Labels: bug

#713 - The executor freezes for two days without any error message

Issue - State: open - Opened by andrewucla about 2 years ago - 7 comments
Labels: bug, moreinfo

#712 - BWA index isn't coppied over with using save-reference option

Issue - State: open - Opened by vsmalladi about 2 years ago - 2 comments
Labels: bug, Azure

#709 - update version for release

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

#706 - Vep Issues: loftee needs version

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

#704 - freec ploidy number -> String

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

#702 - Output from ascat not stable

Issue - State: closed - Opened by asp8200 about 2 years ago - 5 comments
Labels: bug

#700 - BAM index (bai) should be provided

Issue - State: closed - Opened by sabrina0701 about 2 years ago - 2 comments
Labels: docs

#699 - Pass target-bed-file to bcftools/stats?

Issue - State: open - Opened by asp8200 about 2 years ago
Labels: enhancement

#698 - fail to run test data

Issue - State: closed - Opened by bioPG about 2 years ago - 1 comment
Labels: bug, moreinfo

#697 - cnv erro

Issue - State: closed - Opened by ld9866 about 2 years ago - 1 comment
Labels: bug, moreinfo

#682 - Deepvariant requires additional cli option for recalibrated BAM files

Issue - State: open - Opened by marchoeppner about 2 years ago
Labels: bug, good first issue

#678 - Azure errors at Map reads step with segementation fault

Issue - State: closed - Opened by vsmalladi about 2 years ago - 1 comment
Labels: bug, moreinfo, Azure

#675 - forgot to cite eager for subway map

Pull Request - State: closed - Opened by FriederikeHanssen about 2 years ago

#674 - tiny memory update + split fastq default value as discussed on slack

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

#673 - Update igenomes sections and final polish of docs

Pull Request - State: closed - Opened by FriederikeHanssen about 2 years ago - 4 comments

#663 - separate ascat and controlfreec ploidy

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

#662 - update with zipped indices

Pull Request - State: closed - Opened by FriederikeHanssen about 2 years ago - 5 comments

#661 - add cnvkit index

Pull Request - State: closed - Opened by FriederikeHanssen about 2 years ago - 4 comments

#660 - Review Comments for release

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

#656 - try leveling everything up

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

#655 - Fix --intervals false

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

#653 - File structure for results should be coherent between reports and preprocessing

Pull Request - State: closed - Opened by FriederikeHanssen about 2 years ago - 3 comments

#648 - PON not correctly validated

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

#647 - Resource Labels

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

#642 - Small ref file issues for ASCAT, Controlfreec, & CNVKIT

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

#616 - TMB

Pull Request - State: open - Opened by FriederikeHanssen over 2 years ago - 8 comments

#612 - mcontainer creation failed

Issue - State: closed - Opened by maxulysse over 2 years ago - 7 comments

#610 - Documentation

Pull Request - State: closed - Opened by FriederikeHanssen over 2 years ago - 23 comments

#565 - create panel of normals with the pipeline

Issue - State: closed - Opened by sabrina0701 over 2 years ago - 1 comment
Labels: enhancement

#552 - Update changelog

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

#548 - [BUG] Mutect2 fails

Issue - State: closed - Opened by bounlu over 2 years ago - 8 comments
Labels: bug, moreinfo

#544 - Fix Mutect2

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

#536 - Add step markduplicates & allow BAM input for all steps

Pull Request - State: closed - Opened by FriederikeHanssen over 2 years ago - 3 comments

#533 - Issue 509 & 313

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

#526 - Fix issue 114

Pull Request - State: closed - Opened by FriederikeHanssen over 2 years ago - 3 comments

#525 - try bcftools with target

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

#524 - Fix intervals

Pull Request - State: closed - Opened by FriederikeHanssen over 2 years ago - 9 comments

#522 - Add VCF QC

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

#513 - Cnv for real now

Pull Request - State: closed - Opened by FriederikeHanssen over 2 years ago - 3 comments

#511 - Merging template updates 2.3.2

Pull Request - State: closed - Opened by FriederikeHanssen over 2 years ago - 8 comments

#498 - Update docs

Pull Request - State: closed - Opened by FriederikeHanssen over 2 years ago - 11 comments

#497 - Refactor Variant Calling

Pull Request - State: closed - Opened by FriederikeHanssen over 2 years ago - 5 comments