Ecosyste.ms: Issues
An open API service for providing issue and pull request metadata for open source projects.
GitHub / nf-core/atacseq issues and pull requests
#340 - implement the bam_csi_index parameter in atacseq pipeline
Issue -
State: open - Opened by BianyunY-ACRD about 1 year ago
Labels: enhancement
#339 - Process terminated for an unknown reason (SLURM)
Issue -
State: open - Opened by hdbeukel about 1 year ago
Labels: bug
#338 - the sample field from the samplesheet is too lenient
Issue -
State: open - Opened by maxulysse about 1 year ago
Labels: bug
#337 - CONTROL description needs clarifications
Issue -
State: open - Opened by mdozmorov about 1 year ago
Labels: enhancement
#336 - Merge template v2.10
Pull Request -
State: closed - Opened by JoseEspinosa about 1 year ago
- 1 comment
#335 - Important! Template update for nf-core/tools v2.10
Pull Request -
State: closed - Opened by nf-core-bot about 1 year ago
#334 - MAKE_GENE_BED making 0kb .bed files
Issue -
State: open - Opened by hcliedtke about 1 year ago
#333 - Revert "DO NOT MERGE yet: Discuss fixes of #164 #168 #169 "
Pull Request -
State: closed - Opened by bjlang about 1 year ago
- 1 comment
#332 - Fix double slash in directory urls
Issue -
State: open - Opened by jhanifen over 1 year ago
- 1 comment
Labels: bug
#331 - Adding peak-calling with Genrich (fix #108) and multi-mapping read analysis
Pull Request -
State: open - Opened by samuelruizperez over 1 year ago
- 1 comment
Labels: enhancement, WIP
#330 - Error executing process > 'NFCORE_ATACSEQ:ATACSEQ:CUSTOM_DUMPSOFTWAREVERSIONS (1)'
Issue -
State: open - Opened by anijudy over 1 year ago
- 1 comment
Labels: bug
#329 - Create samplesheet_with_control.csv
Pull Request -
State: closed - Opened by bjlang over 1 year ago
- 1 comment
#328 - Add consistent support of .csi indices as alternative to .bai
Pull Request -
State: closed - Opened by bjlang over 1 year ago
- 1 comment
#327 - CSI bam index not working
Issue -
State: open - Opened by heathfuqua over 1 year ago
- 1 comment
Labels: bug
#326 - Bump version 2.2.0dev
Pull Request -
State: closed - Opened by JoseEspinosa over 1 year ago
- 1 comment
#325 - Update release date (DO NOT CLOSE UNTIL RELEASED IS DONE)
Pull Request -
State: closed - Opened by JoseEspinosa over 1 year ago
- 2 comments
#324 - Dev -> Master for 2.1.2 release
Pull Request -
State: closed - Opened by JoseEspinosa over 1 year ago
- 1 comment
#323 - Bump version 2.1.2
Pull Request -
State: closed - Opened by JoseEspinosa over 1 year ago
- 1 comment
#322 - fasta parameter required when using nf-core launch even if --genome is provided
Issue -
State: closed - Opened by JoseEspinosa over 1 year ago
- 1 comment
Labels: bug
#321 - Fixes
Pull Request -
State: closed - Opened by JoseEspinosa over 1 year ago
- 1 comment
#320 - update homer/annotatepeaks from nf-core/modules
Pull Request -
State: closed - Opened by lnblum over 1 year ago
- 3 comments
#319 - Bump pipeline version to 2.2.0dev
Pull Request -
State: closed - Opened by JoseEspinosa over 1 year ago
- 1 comment
#318 - [Question]: macs2 callpeak outputs - narrowPeak vs broadPeak
Issue -
State: closed - Opened by tamuanand over 1 year ago
- 2 comments
#317 - [Question]: FRiP score calculation
Issue -
State: closed - Opened by tamuanand over 1 year ago
- 1 comment
#316 - Patch release 2.1.1
Pull Request -
State: closed - Opened by JoseEspinosa over 1 year ago
- 1 comment
#315 - Bump pipeline version to 2.2.0dev
Pull Request -
State: closed - Opened by JoseEspinosa over 1 year ago
- 1 comment
#314 - Fix multiqc_logo in nextflow_schema
Pull Request -
State: closed - Opened by JoseEspinosa over 1 year ago
- 1 comment
#313 - Apply review suggestions
Pull Request -
State: closed - Opened by JoseEspinosa over 1 year ago
- 1 comment
#312 - Get rid of checkIfExists for params paths
Pull Request -
State: closed - Opened by JoseEspinosa over 1 year ago
- 1 comment
#311 - Dev -> Master for 2.1.0 release
Pull Request -
State: closed - Opened by JoseEspinosa over 1 year ago
- 2 comments
#310 - Bump pipeline version to 2.1.0
Pull Request -
State: closed - Opened by JoseEspinosa over 1 year ago
- 1 comment
#309 - Add read group tag to bowtie2 bams
Pull Request -
State: closed - Opened by JoseEspinosa over 1 year ago
- 1 comment
#308 - Update modules
Pull Request -
State: closed - Opened by bjlang over 1 year ago
- 1 comment
#307 - Updates
Pull Request -
State: closed - Opened by JoseEspinosa over 1 year ago
- 1 comment
#306 - ERROR ~ A process input channel evaluates to null -- Invalid declaration ` val mito_name`
Issue -
State: closed - Opened by JiahuaQu over 1 year ago
- 3 comments
Labels: bug, duplicate
#305 - ERROR ~ Cannot find latest version of nf-validation plugin
Issue -
State: closed - Opened by JiahuaQu over 1 year ago
- 4 comments
#304 - Updates
Pull Request -
State: closed - Opened by JoseEspinosa over 1 year ago
- 1 comment
#303 - '--read_length' and '--macs_gsize' Setting Confusion
Issue -
State: closed - Opened by anijudy over 1 year ago
- 4 comments
Labels: enhancement, documentation
#302 - Process `NFCORE_ATACSEQ:ATACSEQ:MERGED_LIBRARY_ATAQV_MKARV` terminated with an error exit status (1)
Issue -
State: closed - Opened by kkim111 over 1 year ago
- 3 comments
Labels: bug
#301 - DO NOT MERGE yet: Discuss fixes of #164 #168 #169
Pull Request -
State: closed - Opened by ktrns over 1 year ago
- 1 comment
#300 - Merge template 2.9
Pull Request -
State: closed - Opened by JoseEspinosa over 1 year ago
- 1 comment
#299 - nf-core atacseq version 2.0 doesn't perform deseq2 pairwise comparison
Issue -
State: closed - Opened by SereFe over 1 year ago
- 2 comments
Labels: question
#298 - Important! Template update for nf-core/tools v2.9
Pull Request -
State: closed - Opened by nf-core-bot over 1 year ago
#297 - Fixes
Pull Request -
State: closed - Opened by JoseEspinosa over 1 year ago
- 1 comment
#296 - BEDTOOLS_GENOMECOV fails when merged bam is too big for piping
Issue -
State: closed - Opened by JoseEspinosa over 1 year ago
- 1 comment
Labels: bug
#295 - Enable again the processing of paired-end files by Chromap
Issue -
State: closed - Opened by JoseEspinosa over 1 year ago
- 2 comments
Labels: enhancement
#294 - Add `ataqv_mito_reference` parameter
Pull Request -
State: closed - Opened by JoseEspinosa over 1 year ago
- 1 comment
#293 - Update modules and subworkflows
Pull Request -
State: closed - Opened by JoseEspinosa over 1 year ago
- 1 comment
#292 - Fixes
Pull Request -
State: closed - Opened by JoseEspinosa over 1 year ago
- 1 comment
#291 - Fix --blacklist error and make fasta always available for IGV
Pull Request -
State: closed - Opened by JoseEspinosa over 1 year ago
- 1 comment
#290 - Errors in MERGED_LIBRARY_BAM_TO_BIGWIG:UCSC_BEDGRAPHTOBIGWIG
Issue -
State: closed - Opened by AAAAAbetter over 1 year ago
- 4 comments
Labels: bug
#289 - Bed file provided using the --blacklist parameter triggers an error
Issue -
State: closed - Opened by JoseEspinosa over 1 year ago
- 1 comment
Labels: duplicate
#288 - Update changelog
Pull Request -
State: closed - Opened by JoseEspinosa over 1 year ago
- 1 comment
#287 - Fix unzip of fasta file and --mito_name parameter error when not provided
Pull Request -
State: closed - Opened by bjlang over 1 year ago
- 1 comment
Labels: bug
#286 - Pipeline error when no --mito_name param is provided
Issue -
State: closed - Opened by JoseEspinosa over 1 year ago
- 1 comment
Labels: bug
#285 - Simplified testing matrix
Pull Request -
State: closed - Opened by adamrtalbot over 1 year ago
- 2 comments
#284 - V2.1 docs
Pull Request -
State: closed - Opened by adamrtalbot over 1 year ago
- 2 comments
#283 - Remove glob from process definition when using ECR container
Pull Request -
State: closed - Opened by adamrtalbot over 1 year ago
- 1 comment
#282 - Release candidate v2.1
Pull Request -
State: closed - Opened by adamrtalbot over 1 year ago
- 2 comments
#281 - Terminated by the external system
Issue -
State: closed - Opened by CLAIRE-cuhk over 1 year ago
- 2 comments
Labels: question
#280 - Add public_aws_ecr profile for using ECR hosted containers
Pull Request -
State: closed - Opened by adamrtalbot over 1 year ago
- 1 comment
#279 - update all modules for correct registry usage
Pull Request -
State: closed - Opened by maxulysse over 1 year ago
- 3 comments
#278 - IGV cannot open the session file
Issue -
State: closed - Opened by ktrns over 1 year ago
- 2 comments
Labels: enhancement, WIP
#277 - zipped fasta file doesn't work
Issue -
State: closed - Opened by rodriguesk over 1 year ago
- 3 comments
Labels: bug
#276 - ATAQV TSS Enrichment Plots Not Rendering Properly
Issue -
State: closed - Opened by ieres-amgen over 1 year ago
- 2 comments
Labels: bug
#275 - Set a default registry outside of profile scope
Pull Request -
State: closed - Opened by maxulysse over 1 year ago
- 2 comments
#274 - Template update nf-core tools v2.8
Pull Request -
State: closed - Opened by JoseEspinosa over 1 year ago
- 1 comment
#273 - Add GRCm39 option to config
Issue -
State: open - Opened by laurenhsu1 over 1 year ago
- 1 comment
Labels: enhancement
#272 - Reduce available memory for Picard Mark Duplicates
Pull Request -
State: open - Opened by ryan-moreno over 1 year ago
- 1 comment
#271 - Important! Template update for nf-core/tools v2.8
Pull Request -
State: closed - Opened by nf-core-bot over 1 year ago
#270 - nf-core download skips 'bowtie2 align' singularity image with container string parsing error
Issue -
State: closed - Opened by JoseEspinosa over 1 year ago
- 1 comment
Labels: bug
#269 - General statistics table in MultiQC report
Issue -
State: closed - Opened by berguner over 1 year ago
- 2 comments
Labels: enhancement
#268 - Blacklist option causes pipeline to fail
Issue -
State: closed - Opened by StevenWingett over 1 year ago
- 3 comments
Labels: bug
#267 - Add metro map
Pull Request -
State: closed - Opened by bjlang over 1 year ago
- 1 comment
#266 - Update metro map
Pull Request -
State: closed - Opened by bjlang over 1 year ago
- 3 comments
#265 - Remove DESeq2 pairwise comparison reference
Pull Request -
State: closed - Opened by bjlang over 1 year ago
- 1 comment
#264 - add metro map
Pull Request -
State: closed - Opened by bjlang over 1 year ago
- 1 comment
#263 - NameError: name 'logger' is not defined
Issue -
State: closed - Opened by kokyriakidis almost 2 years ago
- 4 comments
#262 - Multiple mithocondial/plastid genomes crashes ataqv
Issue -
State: closed - Opened by maltesemike almost 2 years ago
- 3 comments
Labels: bug
#261 - Modules update
Pull Request -
State: closed - Opened by robsyme almost 2 years ago
- 2 comments
#260 - I have enough memory, but still got 'exceeds available memory' error
Issue -
State: closed - Opened by hyjforesight almost 2 years ago
- 1 comment
Labels: bug
#259 - Add support for optional control data analog to nf-core/chipseq
Pull Request -
State: closed - Opened by bjlang almost 2 years ago
- 1 comment
#258 - Add support for optional control data analog to nf-core/chipseq
Pull Request -
State: closed - Opened by bjlang almost 2 years ago
- 2 comments
#257 - Update nextflow_schema.json
Pull Request -
State: closed - Opened by dangeles almost 2 years ago
- 2 comments
#256 - Robustness: modules/nf-core/bwa/mem/main.nf
Issue -
State: closed - Opened by hukai916 almost 2 years ago
- 2 comments
Labels: bug
#255 - Can not "parse container string"
Issue -
State: closed - Opened by hukai916 almost 2 years ago
- 7 comments
Labels: bug, duplicate
#254 - Cannot upgrade to 2.0 because of uncommitted changes
Issue -
State: closed - Opened by taylordm almost 2 years ago
- 3 comments
Labels: question
#253 - Merge template v2.7.2
Pull Request -
State: closed - Opened by JoseEspinosa almost 2 years ago
- 4 comments
#252 - Important! Template update for nf-core/tools v2.7.2
Pull Request -
State: closed - Opened by nf-core-bot almost 2 years ago
#251 - Merge template v2.7.1
Pull Request -
State: closed - Opened by JoseEspinosa almost 2 years ago
- 2 comments
#250 - Important! Template update for nf-core/tools v2.7.1
Pull Request -
State: closed - Opened by nf-core-bot almost 2 years ago
#249 - nf-core modules update bowtie2/align
Pull Request -
State: closed - Opened by maxulysse almost 2 years ago
- 2 comments
#248 - Revert Channel.of logic to deal with genome indices
Pull Request -
State: closed - Opened by drpatelh almost 2 years ago
#247 - MultiQC report fixes
Pull Request -
State: closed - Opened by drpatelh almost 2 years ago
#246 - Final pre-release fixes
Pull Request -
State: closed - Opened by drpatelh almost 2 years ago
#245 - Dev
Pull Request -
State: closed - Opened by bjlang almost 2 years ago
- 1 comment
#244 - Fixes indexes staging and chromap
Pull Request -
State: closed - Opened by JoseEspinosa almost 2 years ago
#243 - Bump pipeline version and other small fixes
Pull Request -
State: closed - Opened by drpatelh almost 2 years ago
- 1 comment
#242 - Fix bwa_index channel cardinality from prepgenome
Pull Request -
State: closed - Opened by robsyme almost 2 years ago
#241 - Refactor and rename filter bam subworkflow
Pull Request -
State: closed - Opened by drpatelh almost 2 years ago
- 1 comment