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
#1073 - CHORES: back to dev
Pull Request -
State: closed - Opened by maxulysse about 1 year ago
- 2 comments
#1072 - Revisit resource requests
Issue -
State: open - Opened by FriederikeHanssen about 1 year ago
#1071 - docs update
Pull Request -
State: closed - Opened by FriederikeHanssen about 1 year ago
#1070 - CHORES: remove version from pictures
Pull Request -
State: closed - Opened by maxulysse about 1 year ago
#1069 - Remove redundant index computation for DeepVariant
Issue -
State: closed - Opened by FriederikeHanssen about 1 year ago
#1068 - Update conda gatk version
Issue -
State: open - Opened by FriederikeHanssen about 1 year ago
#1067 - Update samtools version for cnvkti
Issue -
State: closed - Opened by FriederikeHanssen about 1 year ago
- 1 comment
#1066 - Future proof Deepvariant output
Issue -
State: open - Opened by FriederikeHanssen about 1 year ago
#1065 - Remove redundant index computation after MarkDuplicates
Issue -
State: closed - Opened by FriederikeHanssen about 1 year ago
Labels: bug
#1064 - Avoid publishing from SENTIEON_GVCFTYPER
Pull Request -
State: closed - Opened by asp8200 about 1 year ago
#1063 - FIX: join duplication for manta/strelka annotation
Pull Request -
State: closed - Opened by maxulysse about 1 year ago
#1062 - FIX: automatic restart from step
Pull Request -
State: closed - Opened by maxulysse about 1 year ago
- 3 comments
#1061 - don't publish genomicsdb files
Pull Request -
State: closed - Opened by FriederikeHanssen about 1 year ago
- 1 comment
#1060 - Issue 1035
Pull Request -
State: closed - Opened by FriederikeHanssen about 1 year ago
#1059 - test out validation plugin
Pull Request -
State: closed - Opened by FriederikeHanssen about 1 year ago
- 2 comments
#1058 - FIX: VCFTOOLS public ecr registry
Pull Request -
State: closed - Opened by maxulysse about 1 year ago
- 2 comments
#1057 - Candidate release 3.2.0
Pull Request -
State: closed - Opened by maxulysse about 1 year ago
- 1 comment
#1056 - CHORES: bump to 3.2.0
Pull Request -
State: closed - Opened by maxulysse about 1 year ago
- 1 comment
#1055 - FIX: pattern for fasta file
Pull Request -
State: closed - Opened by maxulysse about 1 year ago
- 1 comment
#1054 - results folder not seen in sarek output
Issue -
State: closed - Opened by olu2016 about 1 year ago
- 4 comments
Labels: bug
#1053 - Refactor joint germline calling
Issue -
State: closed - Opened by maxulysse about 1 year ago
Labels: PR opened
#1052 - Update VEP version
Issue -
State: closed - Opened by stfacc about 1 year ago
- 1 comment
Labels: bug
#1051 - CHORES: modules update
Pull Request -
State: closed - Opened by maxulysse about 1 year ago
- 1 comment
#1050 - Disable GATK filters when joint calling
Pull Request -
State: closed - Opened by amizeranschi about 1 year ago
- 4 comments
#1049 - Allow genotyping germline sites with Mutect 2
Issue -
State: open - Opened by lbeltrame about 1 year ago
- 2 comments
Labels: enhancement
#1048 - Input validation fixes
Pull Request -
State: closed - Opened by FriederikeHanssen about 1 year ago
- 1 comment
#1047 - Update Sentieon-modules
Issue -
State: closed - Opened by asp8200 about 1 year ago
Labels: enhancement
#1046 - Avoid redundant index-generation in Sentieon-flow.
Issue -
State: closed - Opened by asp8200 about 1 year ago
Labels: enhancement
#1045 - Adds public_aws_ecr profile for using ECR hosted images.
Pull Request -
State: closed - Opened by adamrtalbot about 1 year ago
- 1 comment
#1044 - Sentieon DNAseq flow
Pull Request -
State: closed - Opened by asp8200 about 1 year ago
- 18 comments
#1043 - FIX: typos
Pull Request -
State: closed - Opened by maxulysse about 1 year ago
- 1 comment
#1042 - Rename channels genotype_intervals
Issue -
State: open - Opened by asp8200 about 1 year ago
Labels: enhancement
#1041 - ADD: new vep_custom_args
Pull Request -
State: closed - Opened by maxulysse about 1 year ago
- 2 comments
#1040 - FIX: dict channel issue when using params.dict
Pull Request -
State: closed - Opened by maxulysse about 1 year ago
- 1 comment
#1039 - Remove concatenate_vcfs tests with singularity
Pull Request -
State: closed - Opened by maxulysse about 1 year ago
- 5 comments
#1038 - Mosdepth in sarek runs default with --fast-mode. Could this be made configurable?
Issue -
State: open - Opened by lasseringstedmark about 1 year ago
- 1 comment
Labels: enhancement
#1037 - Investigate failing concatenate_vcfs singularity tests
Issue -
State: closed - Opened by maxulysse about 1 year ago
- 8 comments
#1036 - Fix fastp v 0.23.3
Issue -
State: open - Opened by maxulysse about 1 year ago
- 3 comments
#1035 - Error with GATK4_GENOMICSDBIMPORT during joint calling: Badly formed genome unclippedLoc: Query interval "[]" is not valid for this input
Issue -
State: closed - Opened by amizeranschi about 1 year ago
- 22 comments
Labels: bug
#1034 - onComplete-Mailing fails when running awsbatch-s3 and attaching multiQC report
Issue -
State: open - Opened by lassefolkersen about 1 year ago
Labels: bug
#1033 - Inquiry Regarding Somatic Analysis and Normal Sample Requirement
Issue -
State: closed - Opened by Sadiki-Noureddine about 1 year ago
- 1 comment
#1032 - update all modules for correct registry usage
Pull Request -
State: closed - Opened by maxulysse about 1 year ago
- 5 comments
#1031 - Update pipeline overview
Pull Request -
State: closed - Opened by adamrtalbot about 1 year ago
- 1 comment
#1030 - Exit status 250 and SIGBUS (0x7) errors on GATK processes
Issue -
State: closed - Opened by lfearnley about 1 year ago
- 11 comments
Labels: bug
#1029 - Stop Sarek as early as possible when input-data has too low quality
Issue -
State: open - Opened by asp8200 about 1 year ago
Labels: enhancement
#1028 - Shared results-folder between different pipeline runs?
Issue -
State: open - Opened by asp8200 about 1 year ago
Labels: enhancement
#1027 - Pytest for VQSR-flow
Issue -
State: closed - Opened by asp8200 about 1 year ago
Labels: enhancement, PR opened
#1026 - warning while running sarek 3.1.2 --step variant_calling
Issue -
State: closed - Opened by FrancisNietzsche about 1 year ago
- 3 comments
Labels: bug
#1025 - Filtering of Haplotypecaller VC should only be done for the single-sample route
Issue -
State: closed - Opened by amizeranschi about 1 year ago
- 7 comments
Labels: bug
#1024 - GATK 4.3.0.0 fatal error has been detected by the Java Runtime Environment
Issue -
State: closed - Opened by kabanowa47 about 1 year ago
- 8 comments
Labels: bug
#1023 - Problem running Strelka due to Python version difference
Issue -
State: open - Opened by Venky2804 about 1 year ago
- 3 comments
Labels: bug
#1022 - Fix input channels for variantrecalibrator
Pull Request -
State: closed - Opened by asp8200 about 1 year ago
- 8 comments
#1021 - Passing `--wes true` intervals to mosdepth?
Issue -
State: closed - Opened by mschubert about 1 year ago
- 5 comments
Labels: bug
#1020 - Error while running ASCAT
Issue -
State: open - Opened by Nour-EddineS about 1 year ago
- 9 comments
Labels: bug, moreinfo
#1019 - Set a default registry outside of profile scope
Pull Request -
State: closed - Opened by maxulysse about 1 year ago
- 4 comments
#1018 - Please add CSI indexing
Issue -
State: open - Opened by brettChapman about 1 year ago
Labels: enhancement
#1017 - Error when running nextflow: ERROR ~ No signature of method: java.util.LinkedList.withInputStream()
Issue -
State: closed - Opened by Chrisdoan9 about 1 year ago
- 2 comments
Labels: bug
#1016 - Error running VQSR in joint VC: nextflow.exception.MissingProcessException: Missing process or function mix
Issue -
State: closed - Opened by amizeranschi about 1 year ago
- 6 comments
Labels: bug
#1015 - Reduce interval groups default for smaller storage consumption
Pull Request -
State: closed - Opened by FriederikeHanssen about 1 year ago
- 2 comments
#1014 - fix genome null with annotation
Pull Request -
State: closed - Opened by maxulysse about 1 year ago
- 1 comment
#1013 - Mutect2 multi sample subworkflow
Pull Request -
State: closed - Opened by berguner about 1 year ago
- 19 comments
#1012 - refactoring
Pull Request -
State: closed - Opened by maxulysse about 1 year ago
- 1 comment
#1011 - CHORES: update TEMPLATE with 2.8
Pull Request -
State: closed - Opened by maxulysse about 1 year ago
- 6 comments
#1010 - Important! Template update for nf-core/tools v2.8
Pull Request -
State: closed - Opened by nf-core-bot about 1 year ago
#1009 - CHORES: update subworkflows
Pull Request -
State: closed - Opened by maxulysse about 1 year ago
- 1 comment
#1008 - Update pytest-workflow.yml
Pull Request -
State: closed - Opened by maxulysse about 1 year ago
- 1 comment
#1007 - Sentieon-haplotyper and joint-germline with Sentieon Genotyper and VQSR
Pull Request -
State: closed - Opened by asp8200 about 1 year ago
- 1 comment
#1006 - Error while running sarek v3.1.2: Not a valid S3 file system provider file attribute view
Issue -
State: closed - Opened by FrancisNietzsche about 1 year ago
- 3 comments
Labels: bug
#1005 - Dev
Pull Request -
State: closed - Opened by asp8200 about 1 year ago
- 1 comment
#1004 - error when providing a bed file for targeted samples
Issue -
State: closed - Opened by albcarrasco about 1 year ago
- 4 comments
Labels: bug
#1003 - Add vep_custom_args params to allow for VEP custom args
Issue -
State: closed - Opened by maxulysse about 1 year ago
- 1 comment
Labels: enhancement
#1002 - Adding sentieon-dedup
Pull Request -
State: closed - Opened by asp8200 about 1 year ago
- 3 comments
#1001 - ERROR while running Sarek (v3.1.2) with test_full profile - couldnt get data from s3://nf-core-awsmegatests/sarek/input
Issue -
State: closed - Opened by jsitarova-dnanexus about 1 year ago
- 4 comments
Labels: bug
#1000 - Environment variable SINGULARITYENV_TMP is set, but APPTAINERENV_TMP is preferred
Issue -
State: open - Opened by JiahuaQu about 1 year ago
- 17 comments
Labels: bug, moreinfo
#999 - How to download reference data and tell the pipeline to locate those data in my customized folder?
Issue -
State: closed - Opened by JiahuaQu about 1 year ago
Labels: enhancement
#998 - Issue 952
Pull Request -
State: closed - Opened by FriederikeHanssen about 1 year ago
- 1 comment
#997 - samplesheet verification failed when running variant_calling step
Issue -
State: open - Opened by paumarc about 1 year ago
- 1 comment
Labels: bug, moreinfo
#996 - Evaluate possible drop-in replacements/additions to the GATK suite
Issue -
State: open - Opened by FriederikeHanssen about 1 year ago
Labels: enhancement
#995 - Check & update reference files
Issue -
State: open - Opened by FriederikeHanssen about 1 year ago
Labels: enhancement
#994 - sentieon-bwamem
Pull Request -
State: closed - Opened by asp8200 about 1 year ago
- 3 comments
#993 - ControlFREEC: Error in plot.window(...) : need finite 'ylim' values
Issue -
State: closed - Opened by hyjforesight about 1 year ago
- 3 comments
Labels: bug
#992 - nf-amazon does not exist
Issue -
State: closed - Opened by JiahuaQu about 1 year ago
Labels: bug
#991 - DRAFT: Adding sentieon-bwamem
Pull Request -
State: closed - Opened by asp8200 about 1 year ago
- 2 comments
#990 - fgbio CallMolecularConsensusReads Exception in thread "main" java.lang.OutOfMemoryError: Java heap space
Issue -
State: open - Opened by smzt over 1 year ago
- 2 comments
Labels: bug
#989 - Add optional capability of adding the BED file into samplesheet
Issue -
State: open - Opened by jaybee84 over 1 year ago
Labels: enhancement
#988 - Updated ascat for reproducibility
Pull Request -
State: closed - Opened by SusiJo over 1 year ago
- 1 comment
#987 - Add Illumina/Hap.py module for germline samples with truth set.
Issue -
State: open - Opened by adamrtalbot over 1 year ago
Labels: enhancement
#986 - Singularity related-problems
Issue -
State: closed - Opened by JaumeBagueCompanys over 1 year ago
- 5 comments
Labels: bug, moreinfo
#985 - ADD: Cache correctly identifies when it needs to be updated
Pull Request -
State: closed - Opened by maxulysse over 1 year ago
- 2 comments
#984 - Need to document snpeff_cache/vep_cache clashes with snpeff_version/vep_version
Issue -
State: open - Opened by FriederikeHanssen over 1 year ago
- 1 comment
Labels: enhancement
#983 - Fix caching for tests on custom runners
Issue -
State: closed - Opened by maxulysse over 1 year ago
Labels: bug
#982 - Remove exit statements
Pull Request -
State: closed - Opened by FriederikeHanssen over 1 year ago
- 9 comments
#981 - ASCAT exome/targeted sequencing resource file generation
Pull Request -
State: closed - Opened by ameynert over 1 year ago
- 7 comments
#980 - Enable multiple ploidy values for controlfreec
Pull Request -
State: open - Opened by FriederikeHanssen over 1 year ago
- 5 comments
#979 - Process requirement exceeds available memory: mutect2
Issue -
State: closed - Opened by Nour-EddineS over 1 year ago
- 2 comments
Labels: bug
#978 - Issue 950: samplesheet validation - no spaces in sample or patient names
Pull Request -
State: closed - Opened by matrulda over 1 year ago
- 4 comments
#977 - sarek v3.1.2 -- error for ascat
Issue -
State: open - Opened by PyGuan over 1 year ago
- 7 comments
#976 - Clean up the schema file
Issue -
State: open - Opened by FriederikeHanssen over 1 year ago
Labels: bug, input validation
#975 - Collection of issues regarding joining on metamaps
Issue -
State: closed - Opened by FriederikeHanssen over 1 year ago
- 2 comments
Labels: bug, metamaps
#974 - Can you add the trimming step?
Issue -
State: closed - Opened by JiahuaQu over 1 year ago
- 3 comments
Labels: enhancement