nf-core/scrnaseq issues and pull requests

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

Pull Request - State: closed - Opened by nf-core-bot about 2 years ago - 5 comments

#189 - Inconsistent default protocol

Issue - State: closed - Opened by martinkim0 about 2 years ago - 3 comments
Labels: bug

#188 - update conversion scripts to auto-detect matrix shape

Issue - State: closed - Opened by fmalmeida about 2 years ago - 3 comments
Labels: enhancement

#187 - STARsolo Workflow Doesn't Output Solo.out counts

Issue - State: open - Opened by sean-at-tessera about 2 years ago - 2 comments
Labels: bug

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

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

#185 - UniverSC aligner

Pull Request - State: closed - Opened by TomKellyGenetics about 2 years ago - 12 comments
Labels: enhancement, Ready for review

#184 - gene symbols for alevin-fry

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

#183 - Enable pipeline-specific institutional configs

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

#182 - Include --expect-cells when using --aligner cellranger

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

#181 - 173 should save reference parameter be boolean

Pull Request - State: closed - Opened by fmalmeida over 2 years ago - 1 comment
Labels: bug, Ready for review

#180 - Add Mermaid Graph to Readme for users

Issue - State: open - Opened by apeltzer over 2 years ago - 1 comment
Labels: enhancement, documentation

#179 - fix skip_fastqc channel generations

Pull Request - State: closed - Opened by fmalmeida over 2 years ago - 1 comment
Labels: bug, Ready for review

#178 - Reduce the number of published files from alevin-fry output

Issue - State: open - Opened by tomsing1 over 2 years ago - 1 comment
Labels: enhancement, good first issue

#177 - --skip_fastqc argument leads to an error

Issue - State: closed - Opened by tomsing1 over 2 years ago - 3 comments
Labels: bug

#176 - 2-pass STAR alignment needs to increase limitSjdbInsertNsj

Issue - State: closed - Opened by tomsing1 over 2 years ago - 3 comments
Labels: bug

#175 - Integrate Cellranger-atac

Pull Request - State: closed - Opened by heylf over 2 years ago - 10 comments
Labels: DO_NOT_MERGE

#174 - Add multiome support (scATAC + scRNA)

Issue - State: open - Opened by heylf over 2 years ago - 13 comments
Labels: enhancement

#173 - Should save_reference parameter be boolean?

Issue - State: closed - Opened by tomsing1 over 2 years ago - 7 comments
Labels: bug

#172 - --fasta and --gtf not recognised

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

#171 - Fixing small bug in check_samplesheet

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

#170 - Add UniverSC aligner to support other technologies

Issue - State: closed - Opened by TomKellyGenetics over 2 years ago - 2 comments
Labels: enhancement

#169 - Pipeline picture based on the nf-core best practice pipe-layout

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

#168 - Add single-nucleus, RNA velocity option on star.

Pull Request - State: closed - Opened by Vivian-chen16 over 2 years ago - 1 comment
Labels: Ready for review

#167 - Exposing --tcc option for kb count

Issue - State: open - Opened by ozill12 over 2 years ago - 3 comments

#166 - updated concurrency groups to match nf-core tools

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

#165 - Fix CI

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

#164 - Params expansion 150

Pull Request - State: closed - Opened by ameynert over 2 years ago - 1 comment
Labels: Ready for review

#163 - autocanceling previous tests when pushing changes

Pull Request - State: closed - Opened by kafkasl over 2 years ago - 4 comments
Labels: Ready for review

#162 - Preset option for star to closely reproduce cellranger's count

Issue - State: open - Opened by Vivian-chen16 over 2 years ago
Labels: enhancement

#161 - Add intronic quantification to star for single nuclei

Issue - State: closed - Opened by Vivian-chen16 over 2 years ago - 5 comments
Labels: enhancement

#160 - Output 10x counts

Pull Request - State: closed - Opened by kafkasl over 2 years ago - 15 comments

#159 - Matrix conversions should provide gene annotations

Issue - State: closed - Opened by ogibson over 2 years ago - 2 comments
Labels: enhancement

#158 - Dev branch failing on test config

Issue - State: closed - Opened by ameynert over 2 years ago - 7 comments
Labels: bug

#157 - Cellenics integration

Pull Request - State: open - Opened by kafkasl over 2 years ago - 3 comments

#156 - Add support to upload scRNAseq files to Cellenics for downstream analysis

Issue - State: open - Opened by kafkasl over 2 years ago - 7 comments
Labels: help wanted

#155 - Bump to 2.1.1dev

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

#154 - Release PR 2.1.0

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

#153 - addition of emptyDrops draftdownstream modules

Pull Request - State: closed - Opened by rlinchangco over 2 years ago - 13 comments
Labels: enhancement

#152 - Error with pyroe at alevin-fry indexing step

Issue - State: closed - Opened by Khajidu over 2 years ago - 15 comments
Labels: bug, help wanted

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

Pull Request - State: closed - Opened by nf-core-bot over 2 years ago - 6 comments

#150 - More columns in samplesheet

Issue - State: closed - Opened by grst over 2 years ago - 8 comments
Labels: enhancement

#149 - repair inconsistency

Pull Request - State: closed - Opened by Khajidu over 2 years ago - 4 comments

#148 - Repair inconsistency

Pull Request - State: closed - Opened by Khajidu over 2 years ago - 4 comments

#147 - Cellranger FastQ file name collision

Issue - State: closed - Opened by berguner over 2 years ago - 6 comments
Labels: bug

#144 - Enable iGenomes

Pull Request - State: closed - Opened by robsyme over 2 years ago - 6 comments

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

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

#141 - Add genomic feature and barcode length option for STAR

Pull Request - State: closed - Opened by Vivian-chen16 over 2 years ago - 7 comments

#139 - Switch from alevin to alevin-fry (with simpleaf)

Pull Request - State: closed - Opened by fmalmeida over 2 years ago - 39 comments
Labels: enhancement

#137 - Support for single nucleus RNA-seq data

Issue - State: closed - Opened by galanisl over 2 years ago - 4 comments
Labels: enhancement

#134 - No matrix file in STAR outputs

Issue - State: closed - Opened by Vivian-chen16 over 2 years ago - 3 comments
Labels: bug

#133 - Parse kallisto non-standard (spliced and unspliced) outputs

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

#129 - Add ATAC-Seq data support

Issue - State: closed - Opened by heylf over 2 years ago - 4 comments
Labels: enhancement

#119 - ngs_tools.gtf.Segment.SegmentError: Invalid segment with kallisto aligner

Issue - State: closed - Opened by zhewa over 2 years ago - 1 comment
Labels: bug

#116 - kallisto subworkflow runs out of memory (reiteration of #38)

Issue - State: closed - Opened by Khajidu over 2 years ago - 11 comments
Labels: bug

#98 - Get Alevin seg fault when reading from sample spreadsheet

Issue - State: closed - Opened by SarahBeecroft almost 3 years ago - 3 comments
Labels: bug

#93 - Switch from alevin to alevin-fry

Issue - State: closed - Opened by grst almost 3 years ago - 21 comments
Labels: enhancement

#91 - Implement tests with nf-test

Issue - State: open - Opened by grst about 3 years ago - 4 comments
Labels: enhancement, quality & consistency

#89 - Automatic conversion to h5ad/seurat files after alignment.

Issue - State: closed - Opened by alexblaessle about 3 years ago - 3 comments
Labels: enhancement

#88 - Chemistry/10X version detection

Issue - State: closed - Opened by alexblaessle about 3 years ago - 2 comments
Labels: enhancement

#86 - Default genomes and genome annotation

Issue - State: closed - Opened by grst about 3 years ago - 2 comments
Labels: enhancement

#82 - Detect and remove cell-free mRNA contamination

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

#81 - Call empty droplets

Issue - State: open - Opened by grst about 3 years ago - 4 comments
Labels: enhancement

#80 - Improve QC reports

Issue - State: open - Opened by grst about 3 years ago - 5 comments
Labels: enhancement

#78 - Alevin workflow cannot handle gzipped genomes or gtf files

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

#75 - Demuxlet/Freemuxlet module

Issue - State: closed - Opened by mikecuoco over 3 years ago - 1 comment
Labels: enhancement

#68 - Add AnnData output process

Issue - State: closed - Opened by Zethson over 3 years ago - 18 comments
Labels: enhancement, good first issue

#66 - Make output compatible with nf-core/scflow

Issue - State: closed - Opened by apeltzer over 3 years ago - 2 comments
Labels: enhancement

#50 - Modules for scrnaseq

Issue - State: closed - Opened by ggabernet almost 4 years ago - 12 comments

#29 - Unknown config attribute `params.genomes.GRCh37.salmon_index`

Issue - State: closed - Opened by winni2k about 5 years ago - 2 comments
Labels: question

#14 - Add RNA Velocity

Issue - State: open - Opened by olgabot over 5 years ago - 6 comments
Labels: enhancement

GitHub / nf-core/scrnaseq issues and pull requests