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

#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

#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

#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

#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

#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