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
#949 - Running the annotation step does not work with the full samplesheet file described on the website or with the variantcalling.csv file generated by the pipeline in a previous step
Issue -
State: closed - Opened by MolPath-Bioinfo over 1 year ago
- 6 comments
Labels: bug, 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
#938 - Process `NFCORE_SAREK:SAREK:GERMLINE_VARIANT_CALLING:RUN_HAPLOTYPECALLER:JOINT_GERMLINE:MERGE_GENOTYPEGVCFS (joint_variant_calling)` terminated with an error exit status (3)
Issue -
State: closed - Opened by nagihayate over 1 year ago
- 16 comments
Labels: bug, metamaps
#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