Ecosyste.ms: Issues

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

GitHub / nf-core/rnavar issues and pull requests

#109 - update all modules

Pull Request - State: closed - Opened by maxulysse 8 months ago - 2 comments

#108 - input file name collision

Issue - State: open - Opened by vivischuch 8 months ago - 5 comments
Labels: bug

#107 - FIX: issues reported on Slack

Pull Request - State: closed - Opened by maxulysse 8 months ago - 1 comment

#106 - fix vep_cache

Pull Request - State: open - Opened by bounlu 9 months ago - 1 comment

#105 - fix ch_dict

Pull Request - State: closed - Opened by bounlu 9 months ago - 1 comment

#104 - temporary fix for #103

Pull Request - State: closed - Opened by bounlu 9 months ago - 1 comment

#103 - `dev` version gets stuck at Launching step

Issue - State: open - Opened by bounlu 9 months ago
Labels: bug

#102 - fix process name SNPEFF_SNPEFF

Pull Request - State: closed - Opened by bounlu 9 months ago - 1 comment

#101 - fix process name for SNPEFF_SNPEFF

Pull Request - State: closed - Opened by bounlu 9 months ago - 1 comment

#100 - fix process name

Pull Request - State: closed - Opened by bounlu 9 months ago

#99 - Gunzipping before STAR alignment on NTFS

Issue - State: closed - Opened by jcdaneshmand 9 months ago - 1 comment
Labels: enhancement

#98 - FEAT: add annotation back

Pull Request - State: closed - Opened by maxulysse 9 months ago - 2 comments

#97 - Important! Template update for nf-core/tools v2.10

Pull Request - State: closed - Opened by nf-core-bot 9 months ago - 2 comments

#96 - Add `trimming` step

Issue - State: open - Opened by bounlu 11 months ago
Labels: enhancement

#95 - Important! Template update for nf-core/tools v2.9

Pull Request - State: closed - Opened by nf-core-bot about 1 year ago - 2 comments

#93 - Singularity container retrieval failed

Issue - State: open - Opened by hakobyansiras about 1 year ago
Labels: bug

#91 - Important! Template update for nf-core/tools v2.8

Pull Request - State: closed - Opened by nf-core-bot about 1 year ago - 1 comment

#90 - GRCh38 gtf file being used even when custom gff file is supplied

Issue - State: open - Opened by davidecarlson about 1 year ago
Labels: bug

#89 - Pipeline test is failing

Issue - State: open - Opened by davidecarlson about 1 year ago - 2 comments
Labels: bug

#88 - MERGE TEMPLATE

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

#87 - `strandedness` field is unnecessary

Issue - State: open - Opened by bounlu over 1 year ago
Labels: bug

#86 - Add UMI spport

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

#84 - ENSEMBLVEP fails after module update

Issue - State: open - Opened by bounlu over 1 year ago - 2 comments
Labels: bug

#83 - Warning about GATK4_HAPLOTYPECALLERGVCF

Issue - State: open - Opened by bounlu over 1 year ago - 1 comment
Labels: bug

#82 - SAMTOOLS_FAIDX can't locate singularity image

Issue - State: open - Opened by PBMCHUGA over 1 year ago - 9 comments
Labels: bug

#81 - Implementing the --AlignIntronMax option for STAR

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

#80 - Important! Template update for nf-core/tools v2.7.2

Pull Request - State: closed - Opened by nf-core-bot over 1 year ago

#79 - Important! Template update for nf-core/tools v2.7.1

Pull Request - State: closed - Opened by nf-core-bot over 1 year ago - 1 comment

#77 - Single cell somatic mutations

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

#76 - Issue with FastQC

Issue - State: open - Opened by jsangalang over 1 year ago

#75 - Download snpeff singularity image failed

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

#74 - Prepared `STARIndex` folder is missing for `GATK/GRCh38`

Issue - State: open - Opened by bounlu over 1 year ago
Labels: bug

#73 - Important! Template update for nf-core/tools v2.6

Pull Request - State: closed - Opened by nf-core-bot almost 2 years ago - 1 comment

#72 - NFCORE_RNAVAR:RNAVAR:SPLITNCIGAR:GATK4_SPLITNCIGARREADS error

Issue - State: open - Opened by gianfilippo almost 2 years ago - 3 comments
Labels: bug

#71 - download_cache.nf not found

Issue - State: open - Opened by gianfilippo almost 2 years ago
Labels: bug

#70 - Important! Template update for nf-core/tools v2.5.1

Pull Request - State: closed - Opened by nf-core-bot almost 2 years ago - 1 comment

#69 - Important! Template update for nf-core/tools v2.5

Pull Request - State: closed - Opened by nf-core-bot almost 2 years ago - 1 comment

#68 - Strandedness

Issue - State: open - Opened by kunstner almost 2 years ago - 1 comment
Labels: enhancement

#67 - Error when running rnavar with --skip_intervallisttools option

Issue - State: open - Opened by RaqManzano almost 2 years ago
Labels: bug

#66 - File name collision error

Issue - State: open - Opened by Jokendo-collab almost 2 years ago - 2 comments
Labels: bug

#65 - Missing STAR index not created automaticaly

Issue - State: open - Opened by kunstner almost 2 years ago - 5 comments
Labels: bug

#64 - Can't find template file dumpsoftwareversions.py

Issue - State: closed - Opened by jackkamm almost 2 years ago - 1 comment

#63 - Optional filter out RNA editing variants

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

#62 - Updated Zenodo DOI

Pull Request - State: closed - Opened by praveenraj2018 about 2 years ago - 1 comment

#61 - Added Zenodo DOI badge

Pull Request - State: closed - Opened by praveenraj2018 about 2 years ago - 3 comments

#60 - Bump version to v1.1.0dev

Pull Request - State: closed - Opened by praveenraj2018 about 2 years ago - 1 comment

#59 - Summary metrics of haplotypecaller.filtered.vcf

Issue - State: open - Opened by ojziff about 2 years ago - 1 comment
Labels: enhancement

#58 - Added release date in CHANGELOG.md

Pull Request - State: closed - Opened by praveenraj2018 about 2 years ago - 1 comment

#57 - Added the release date

Pull Request - State: closed - Opened by praveenraj2018 about 2 years ago - 1 comment

#56 - Addressed the review comments

Pull Request - State: closed - Opened by praveenraj2018 about 2 years ago - 1 comment

#55 - Genome files clashing

Issue - State: open - Opened by ojziff about 2 years ago - 1 comment
Labels: bug

#54 - incorrect merging (CAT_FASTQ) of different samples

Issue - State: closed - Opened by ojziff about 2 years ago - 3 comments
Labels: bug

#53 - Prepare release 1.0.0

Pull Request - State: closed - Opened by praveenraj2018 about 2 years ago - 8 comments

#52 - Bump version to 1.0.0; Edit CHANGELOG.md

Pull Request - State: closed - Opened by praveenraj2018 about 2 years ago - 1 comment

#51 - Minor corrections in documentation

Pull Request - State: closed - Opened by praveenraj2018 about 2 years ago - 1 comment

#50 - produce g.vcf file

Issue - State: open - Opened by SarahMaman about 2 years ago - 1 comment
Labels: enhancement

#49 - Latest GATK version

Pull Request - State: closed - Opened by praveenraj2018 about 2 years ago - 1 comment

#48 - Important! Template update for nf-core/tools v2.4

Pull Request - State: closed - Opened by nf-core-bot about 2 years ago

#47 - Review feedback corrections

Pull Request - State: closed - Opened by praveenraj2018 about 2 years ago - 1 comment

#46 - Additional review comments addressed

Pull Request - State: closed - Opened by praveenraj2018 about 2 years ago - 1 comment

#45 - Review corrections

Pull Request - State: closed - Opened by praveenraj2018 about 2 years ago - 1 comment

#44 - Simplified splitNCigar subworkflow with bam_csi_index fix

Pull Request - State: closed - Opened by praveenraj2018 about 2 years ago - 2 comments

#43 - CSI index support and other minor fixes

Pull Request - State: closed - Opened by praveenraj2018 about 2 years ago - 3 comments

#42 - samplesheet check for distributed run

Issue - State: closed - Opened by AnotherSimon about 2 years ago - 4 comments
Labels: bug

#41 - Allow bam files to be added as input to rnavar workflow

Issue - State: open - Opened by jaybee84 about 2 years ago - 3 comments
Labels: enhancement

#40 - Exonic bed other fixes

Pull Request - State: closed - Opened by praveenraj2018 about 2 years ago - 3 comments

#39 - PSEUDO PR - DO NOT MERGE

Pull Request - State: closed - Opened by maxulysse about 2 years ago - 12 comments

#38 - Issue fix and minor additions

Pull Request - State: closed - Opened by praveenraj2018 about 2 years ago - 1 comment

#37 - Fix: Call genome index if star_index is not provided

Pull Request - State: closed - Opened by praveenraj2018 about 2 years ago - 1 comment

#36 - fix: renamed meta with interval BaseName to work correctly in MergeVCFs

Pull Request - State: closed - Opened by praveenraj2018 over 2 years ago - 1 comment

#35 - Doc final updates

Pull Request - State: closed - Opened by praveenraj2018 over 2 years ago - 1 comment

#34 - Somatic Variant Calling (Tumor-Normal & Tumor-Only)

Issue - State: closed - Opened by JasperO98 over 2 years ago - 1 comment
Labels: enhancement

#33 - Dsl2 updates

Pull Request - State: closed - Opened by praveenraj2018 over 2 years ago - 1 comment

#32 - nf-core template merge 2.3.2

Pull Request - State: closed - Opened by praveenraj2018 over 2 years ago - 1 comment

#31 - nf-core template merge 2.3.2

Pull Request - State: closed - Opened by praveenraj2018 over 2 years ago - 1 comment

#30 - Nf core template merge 2.3.2

Pull Request - State: closed - Opened by praveenraj2018 over 2 years ago - 1 comment

#29 - Important! Template update for nf-core/tools v2.3.2

Pull Request - State: closed - Opened by nf-core-bot over 2 years ago

#28 - Dsl update2

Pull Request - State: closed - Opened by praveenraj2018 over 2 years ago - 7 comments

#27 - Important! Template update for nf-core/tools v2.3

Pull Request - State: closed - Opened by nf-core-bot over 2 years ago

#26 - Cannot overwrite some params

Issue - State: open - Opened by m3hdad over 2 years ago
Labels: bug

#25 - grep feature name for BED interval list

Pull Request - State: closed - Opened by m3hdad over 2 years ago - 2 comments

#24 - GffGtf fix

Pull Request - State: closed - Opened by m3hdad over 2 years ago - 1 comment

#23 - added: skip_baserecalibration

Pull Request - State: closed - Opened by praveenraj2018 over 2 years ago - 1 comment

#22 - Updated documentation

Pull Request - State: closed - Opened by praveenraj2018 over 2 years ago - 1 comment

#21 - GFF to GTF conversion is ignored, GTF is required!

Issue - State: closed - Opened by m3hdad over 2 years ago - 2 comments
Labels: bug

#20 - SIFT missense predictions for genomes

Issue - State: open - Opened by m3hdad over 2 years ago
Labels: enhancement

#19 - snp/indel databases are required

Issue - State: closed - Opened by m3hdad over 2 years ago
Labels: bug

#18 - snp/indel databases are required [issue 001]

Pull Request - State: closed - Opened by m3hdad over 2 years ago - 1 comment

#17 - Fix: samtools faidx issue with genome.fa

Pull Request - State: closed - Opened by praveenraj2018 over 2 years ago - 1 comment

#16 - DSL2 version

Pull Request - State: closed - Opened by praveenraj2018 over 2 years ago - 1 comment

#15 - Important! Template update for nf-core/tools v2.2

Pull Request - State: closed - Opened by nf-core-bot over 2 years ago

#14 - Added rnavar custom config profile

Pull Request - State: closed - Opened by praveenraj2018 over 2 years ago - 1 comment

#13 - Docs other fixes

Pull Request - State: closed - Opened by praveenraj2018 over 2 years ago - 5 comments

#11 - fix: cache variable

Pull Request - State: closed - Opened by praveenraj2018 over 2 years ago - 1 comment

#10 - Parallel proc

Pull Request - State: closed - Opened by praveenraj2018 over 2 years ago - 1 comment