Ecosyste.ms: Issues
An open API service for providing issue and pull request metadata for open source projects.
GitHub / nf-core/scrnaseq issues and pull requests
#290 - Tests for cellranger-arc
Issue -
State: open - Opened by grst about 1 year ago
Labels: enhancement, quality & consistency
#289 - Update or remove universc
Issue -
State: open - Opened by grst about 1 year ago
- 1 comment
Labels: enhancement, quality & consistency
#288 - Update modules and fix missing variable error
Pull Request -
State: open - Opened by grst about 1 year ago
- 3 comments
#287 - Bump version to 2.6.0dev
Pull Request -
State: closed - Opened by grst about 1 year ago
- 1 comment
#286 - GHGA contribution to README
Pull Request -
State: closed - Opened by heylf about 1 year ago
- 1 comment
#285 - Use nf-validation plugin
Issue -
State: open - Opened by grst about 1 year ago
Labels: quality & consistency
#284 - Fix time limits
Pull Request -
State: closed - Opened by grst about 1 year ago
- 1 comment
#283 - Release v2.5.0
Pull Request -
State: closed - Opened by grst about 1 year ago
- 5 comments
#282 - bump version to 2.5.0 for release
Pull Request -
State: closed - Opened by grst about 1 year ago
- 1 comment
#281 - increase time limits
Pull Request -
State: closed - Opened by grst about 1 year ago
- 1 comment
#280 - Bump up kb to 0.28.0
Issue -
State: open - Opened by gennadyFauna about 1 year ago
- 2 comments
Labels: enhancement
#279 - Important! Template update for nf-core/tools v2.11.1
Pull Request -
State: closed - Opened by nf-core-bot about 1 year ago
- 2 comments
#278 - Important! Template update for nf-core/tools v2.11
Pull Request -
State: closed - Opened by nf-core-bot about 1 year ago
- 1 comment
#277 - Crash when specifying existing --star_index using star aligner
Issue -
State: open - Opened by ffmmulder about 1 year ago
- 2 comments
Labels: bug
#276 - Solve issue #247 Adding cellrangermulti subworkflow
Pull Request -
State: open - Opened by fmalmeida about 1 year ago
- 2 comments
#275 - exceeded running time limit (8h)
Issue -
State: closed - Opened by luozhy88 over 1 year ago
- 3 comments
Labels: bug
#274 - Adding cellranger-arc (multiome scRNA-seq + scATAC support)
Pull Request -
State: closed - Opened by heylf over 1 year ago
- 13 comments
Labels: Ready for review
#273 - Better support for custom chemistries
Pull Request -
State: closed - Opened by grst over 1 year ago
- 1 comment
#272 - Multi-omics support (meta-issue)
Issue -
State: open - Opened by grst over 1 year ago
- 1 comment
Labels: enhancement
#271 - Bump version to 2.5.0dev
Pull Request -
State: closed - Opened by grst over 1 year ago
- 1 comment
#270 - Update modules
Pull Request -
State: closed - Opened by grst over 1 year ago
- 4 comments
#269 - Important! Template update for nf-core/tools v2.10
Pull Request -
State: closed - Opened by nf-core-bot over 1 year ago
- 2 comments
#268 - Release v2.4.1
Pull Request -
State: closed - Opened by grst over 1 year ago
- 2 comments
#267 - Fix 263
Pull Request -
State: closed - Opened by grst over 1 year ago
- 4 comments
#266 - bump version for patch release
Pull Request -
State: closed - Opened by grst over 1 year ago
- 1 comment
#265 - Autorenaming of files in new cellranger module leads to erroneous renaming of sample ID containing R1 in it, like in SRR ids
Issue -
State: closed - Opened by BurtonChia over 1 year ago
- 2 comments
Labels: bug
#264 - Switch to use central nf-core modules
Issue -
State: open - Opened by pinin4fjords over 1 year ago
Labels: enhancement, quality & consistency
#263 - Fix whitelist logic for Drop-seq
Issue -
State: closed - Opened by FelixKrueger over 1 year ago
Labels: bug, enhancement
#262 - Universc options for BD data
Issue -
State: closed - Opened by sclan over 1 year ago
- 2 comments
Labels: bug
#261 - fix cellranger filename check
Pull Request -
State: closed - Opened by grst over 1 year ago
- 3 comments
#260 - bump version to 2.5.0dev
Pull Request -
State: closed - Opened by grst over 1 year ago
- 1 comment
#259 - remove validationSchemaIgnoreParams warning with test profile
Pull Request -
State: closed - Opened by maxulysse over 1 year ago
- 1 comment
#258 - smartseq 1/2 support
Issue -
State: closed - Opened by matq007 over 1 year ago
- 1 comment
Labels: enhancement
#257 - Error converting mtx to seurat when using singularity
Issue -
State: closed - Opened by rhodesch over 1 year ago
- 2 comments
Labels: bug
#256 - Release v2.4.0
Pull Request -
State: closed - Opened by grst over 1 year ago
- 6 comments
#255 - Bump version for release
Pull Request -
State: closed - Opened by grst over 1 year ago
- 1 comment
#254 - fix typo causing empty version imformation for mtx_conversion subwork…
Pull Request -
State: closed - Opened by shinthor over 1 year ago
- 2 comments
#253 - Error at SIMPLEAF_INDEX for user supplied genome/annotation
Issue -
State: open - Opened by jeremymsimon over 1 year ago
Labels: bug
#252 - Remove duplicate registry settings in nextflow.config
Pull Request -
State: closed - Opened by adamrtalbot over 1 year ago
- 1 comment
#251 - samplesheet with 3 columns
Issue -
State: closed - Opened by rhodesch over 1 year ago
- 1 comment
Labels: bug
#250 - Update to v2.3.2
Pull Request -
State: closed - Opened by chris-cheshire over 1 year ago
- 2 comments
#249 - Launch tool not working for various pipelines, including scRNAseq and RNAseq.
Issue -
State: closed - Opened by denisthieffry over 1 year ago
- 2 comments
Labels: bug
#248 - Failed to pull singularity image
Issue -
State: closed - Opened by Juassis over 1 year ago
- 6 comments
Labels: bug
#247 - Support for 10x FFPE scRNA
Issue -
State: open - Opened by pakiessling over 1 year ago
- 3 comments
Labels: enhancement
#246 - Update cellranger module
Pull Request -
State: closed - Opened by grst over 1 year ago
- 2 comments
#245 - Important! Template update for nf-core/tools v2.9
Pull Request -
State: closed - Opened by nf-core-bot over 1 year ago
- 1 comment
#244 - Add cellranger to multiqc report
Pull Request -
State: closed - Opened by grst over 1 year ago
- 1 comment
#243 - ERROR ~ `NFCORE_SCRNASEQ:SCRNASEQ:MTX_CONVERSION:MTX_TO_SEURAT` input file name collision
Issue -
State: closed - Opened by rhodesch over 1 year ago
- 4 comments
Labels: bug
#242 - Remove public_aws_ecr profile
Pull Request -
State: closed - Opened by adamrtalbot over 1 year ago
- 2 comments
#241 - Cellranger / spaceranger input file handling
Issue -
State: closed - Opened by grst over 1 year ago
- 2 comments
Labels: enhancement
#240 - Update public_aws_ecr.config
Pull Request -
State: closed - Opened by maxulysse over 1 year ago
- 1 comment
#239 - fix (231): Null object accessed in multiqc channel
Pull Request -
State: closed - Opened by adamrtalbot over 1 year ago
- 2 comments
#238 - scRNA-seq with Cellranger fails at Seurat conversion stage
Issue -
State: closed - Opened by FelixKrueger over 1 year ago
- 2 comments
Labels: bug
#237 - Add singularity.registry = 'quay.io' and bump NF version to 23.04.0
Pull Request -
State: closed - Opened by drpatelh over 1 year ago
- 1 comment
#236 - Extend Pipeline to analyze CAR-T-cell datasets
Issue -
State: closed - Opened by Karantea over 1 year ago
- 1 comment
#235 - Option to skip postprocessing
Issue -
State: open - Opened by zvittorio over 1 year ago
- 2 comments
Labels: enhancement
#234 - Dev -> Master for 2.3.2 release
Pull Request -
State: closed - Opened by drpatelh over 1 year ago
- 1 comment
#233 - Move containers for pipeline to quay.io
Pull Request -
State: closed - Opened by drpatelh over 1 year ago
- 1 comment
#232 - Fix_file_collision_when_using_cellranger
Pull Request -
State: closed - Opened by adamrtalbot over 1 year ago
- 1 comment
#231 - Null object when running MultiQC
Issue -
State: closed - Opened by adamrtalbot over 1 year ago
- 1 comment
Labels: bug
#230 - Universc "essential container in task exited"
Issue -
State: open - Opened by adamrtalbot over 1 year ago
- 2 comments
Labels: bug
#229 - Cellranger fails to write _jobinfo.tmp
Issue -
State: closed - Opened by adamrtalbot over 1 year ago
- 3 comments
Labels: bug
#228 - Remove globs from ecr profile
Pull Request -
State: closed - Opened by adamrtalbot over 1 year ago
- 2 comments
#227 - Update docs for release 2.3.1
Pull Request -
State: closed - Opened by adamrtalbot over 1 year ago
- 2 comments
#226 - Release candidate v2.3.1
Pull Request -
State: closed - Opened by adamrtalbot over 1 year ago
- 1 comment
#225 - Public aws ecr profile
Pull Request -
State: closed - Opened by adamrtalbot over 1 year ago
- 1 comment
#224 - Fix code comment
Pull Request -
State: closed - Opened by stan0610 almost 2 years ago
#223 - Dev -> Master for v2.3.0 release
Pull Request -
State: closed - Opened by robsyme almost 2 years ago
- 1 comment
#222 - Readying for 2.3.0 release
Pull Request -
State: closed - Opened by robsyme almost 2 years ago
- 1 comment
#221 - Important! Template update for nf-core/tools v2.8
Pull Request -
State: closed - Opened by nf-core-bot almost 2 years ago
- 1 comment
#220 - Ensure that starsolo outputs channel that matches others, including meta map
Pull Request -
State: closed - Opened by robsyme almost 2 years ago
- 1 comment
#219 - Remove unused --bustools_correct and --skip_bustools and fix bugs in schema defaults
Pull Request -
State: closed - Opened by drpatelh almost 2 years ago
- 1 comment
#218 - accept custom geometry strings when `alevin` is used as aligner
Issue -
State: closed - Opened by suhrig almost 2 years ago
- 17 comments
Labels: enhancement
#217 - Cellranger arc
Pull Request -
State: closed - Opened by heylf almost 2 years ago
- 1 comment
Labels: DO_NOT_MERGE
#216 - 211 samplesheet error in v220 when more than 3 fields are present
Pull Request -
State: closed - Opened by fmalmeida almost 2 years ago
- 2 comments
#215 - Fix #214
Pull Request -
State: closed - Opened by sandrocarollo almost 2 years ago
- 6 comments
#214 - Auto rename fastq files for cellranger input
Issue -
State: closed - Opened by vjmarteau almost 2 years ago
- 2 comments
Labels: enhancement
#213 - test1
Pull Request -
State: closed - Opened by abyssum almost 2 years ago
- 1 comment
#212 - Support additional sequencing platforms through seqspec
Issue -
State: open - Opened by grst almost 2 years ago
Labels: enhancement
#211 - Samplesheet error in v2.2.0 when more than 3 fields are present
Issue -
State: closed - Opened by davidecarlson almost 2 years ago
- 4 comments
Labels: bug
#210 - bump version to 2.3.0dev
Pull Request -
State: closed - Opened by grst almost 2 years ago
- 2 comments
#209 - Adding universc to pipeline picture
Pull Request -
State: closed - Opened by heylf almost 2 years ago
- 3 comments
#208 - Update cellranger_mkref please
Issue -
State: closed - Opened by jhgraber almost 2 years ago
- 1 comment
Labels: bug
#207 - update readme
Pull Request -
State: closed - Opened by grst almost 2 years ago
- 2 comments
#206 - bump version
Pull Request -
State: closed - Opened by fmalmeida almost 2 years ago
- 1 comment
#205 - Update modules
Pull Request -
State: closed - Opened by grst almost 2 years ago
- 1 comment
#204 - Fix Seurat container
Pull Request -
State: closed - Opened by grst almost 2 years ago
- 1 comment
#203 - v2.2.0 release
Pull Request -
State: closed - Opened by grst almost 2 years ago
- 2 comments
#202 - fix txp2gene retrieval bug when salmon_index is supplied
Pull Request -
State: closed - Opened by azedine-healx almost 2 years ago
- 1 comment
#201 - Update all modules, fix template points
Pull Request -
State: closed - Opened by apeltzer almost 2 years ago
- 1 comment
#200 - Enrich DESeq QC output
Issue -
State: closed - Opened by RoganGrant almost 2 years ago
Labels: enhancement
#199 - possible bug with Wave containers and process `MTX_TO_SEURAT`?
Issue -
State: closed - Opened by klkeys almost 2 years ago
- 12 comments
Labels: bug
#198 - Fix 191 and update to template 2.7.2
Pull Request -
State: closed - Opened by apeltzer almost 2 years ago
- 4 comments
#197 - Fix 196
Pull Request -
State: closed - Opened by apeltzer about 2 years ago
- 2 comments
#196 - Increase time limit for alevinQC
Issue -
State: closed - Opened by FelixKrueger about 2 years ago
- 3 comments
Labels: bug
#195 - The input FastQ file names produce an error in the pipeline execution - cellranger error
Issue -
State: closed - Opened by lewis9914 about 2 years ago
- 2 comments
Labels: bug
#194 - Format GTF before SIMPLEAF_INDEX
Pull Request -
State: closed - Opened by robsyme about 2 years ago
- 3 comments
#193 - nf-core/tools=2.7.2 downloading scrnaseq: Cannot parse container string
Issue -
State: closed - Opened by mschubert about 2 years ago
- 5 comments
Labels: bug
#192 - Pipeline competed with errors
Issue -
State: closed - Opened by KeLi1018 about 2 years ago
- 5 comments
Labels: bug
#191 - pyroe failed to return succesfully ExitStatus(unix_wait_status(256))
Issue -
State: closed - Opened by lfperales about 2 years ago
- 30 comments
Labels: bug