nf-core/airrflow issues and pull requests

#300 - Fetch other databases than IMGT: AIRR reference set

Issue - State: open - Opened by ggabernet 9 months ago
Labels: enhancement

#299 - Provide profile for NEB and TAKARA protocols

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

#298 - Add regions translations to final repertoire table

Issue - State: open - Opened by ggabernet 9 months ago
Labels: enhancement

#297 - Diversity reports

Issue - State: open - Opened by ggabernet 9 months ago
Labels: bug, enchantr

#296 - Update immcantation container

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

#295 - Fix sequence plot in airrflow report

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

#294 - merge template updates

Pull Request - State: closed - Opened by ggabernet 10 months ago - 1 comment

#293 - clonal_threshold accepts multiple values in nextflow_schema.json

Pull Request - State: closed - Opened by adamrtalbot 10 months ago - 5 comments

#292 - Invalid nextflow_schema.json using list type.

Issue - State: closed - Opened by adamrtalbot 10 months ago
Labels: bug

#291 - Important! Template update for nf-core/tools v2.11.1

Pull Request - State: closed - Opened by nf-core-bot 10 months ago

#290 - Important! Template update for nf-core/tools v2.11

Pull Request - State: closed - Opened by nf-core-bot 10 months ago - 1 comment

#289 - Cellranger vdj

Pull Request - State: open - Opened by mapo9 10 months ago - 1 comment

#288 - fixed comment im changeo_convertdb_fasta

Pull Request - State: open - Opened by mapo9 10 months ago - 2 comments

#287 - Remove FilterQuality silent fail

Pull Request - State: closed - Opened by ggabernet 11 months ago - 1 comment

#286 - Apply reviews

Pull Request - State: closed - Opened by ggabernet 11 months ago - 1 comment

#285 - Missing output file(s) `*_R1_primers-pass.fastq`

Issue - State: closed - Opened by LiuH2020 12 months ago - 3 comments
Labels: bug

#284 - Use cached reference data by default

Pull Request - State: closed - Opened by ggabernet 12 months ago - 1 comment

#283 - fix validate params

Pull Request - State: closed - Opened by ggabernet 12 months ago - 1 comment

#282 - Release 3.2.0

Pull Request - State: closed - Opened by ggabernet 12 months ago - 1 comment

#281 - small fixes

Pull Request - State: closed - Opened by ggabernet 12 months ago - 1 comment

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

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

#279 - merge nf-core tools template update

Pull Request - State: closed - Opened by ggabernet about 1 year ago - 1 comment

#278 - Update to Enchantr 0.1.7

Pull Request - State: closed - Opened by ggabernet about 1 year ago - 3 comments

#277 - Analyzing BCR Rep-Seq Data in nf-core/airrflow Without Primer Information

Issue - State: closed - Opened by pengjiao about 1 year ago - 2 comments
Labels: enhancement

#276 - Short term fix issues Dowser singularity container

Pull Request - State: closed - Opened by ggabernet about 1 year ago - 1 comment

#275 - test data failing

Issue - State: closed - Opened by andreiprodan about 1 year ago - 3 comments
Labels: bug

#274 - Imgt url fix

Pull Request - State: closed - Opened by mdeboth about 1 year ago - 2 comments

#273 - IMGT/GENE-DB downloads failing

Issue - State: closed - Opened by mdeboth about 1 year ago - 2 comments
Labels: bug

#272 - Report findthreshold should report chosen threshold

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

#271 - samplesheet check make character

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

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

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

#269 - Update EnchantR to 0.1.3

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

#268 - Parametrize findthreshold

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

#267 - Dev

Pull Request - State: closed - Opened by ssnn-airr over 1 year ago - 2 comments

#266 - Add assembled check to samplesheet, fix report use read_rearrangement

Pull Request - State: closed - Opened by ggabernet over 1 year ago - 2 comments

#265 - Apply review corrections and tool version update

Pull Request - State: closed - Opened by ggabernet over 1 year ago - 2 comments

#264 - Add public_aws_ecr profile

Pull Request - State: closed - Opened by adamrtalbot over 1 year ago - 2 comments

#263 - bump versions to 3.1.0

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

#262 - 3.1.0 release: Template update and minor bugfixes

Pull Request - State: closed - Opened by ggabernet over 1 year ago - 2 comments

#261 - Changeo Assigngenes format airr

Pull Request - State: closed - Opened by ggabernet over 1 year ago - 1 comment
Labels: do not merge

#260 - Update immcantation-devel changes

Pull Request - State: closed - Opened by ggabernet over 1 year ago - 2 comments

#259 - Immcantation devel

Pull Request - State: closed - Opened by ggabernet over 1 year ago - 1 comment
Labels: ready for review and merge

#258 - Report fix and other bugfixes

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

#257 - Identify / remove spaces in fields in the metadata table

Issue - State: closed - Opened by ggabernet over 1 year ago - 1 comment
Labels: enhancement

#256 - Template update nf-core tools v2.8

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

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

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

#254 - dowser updates

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

#253 - Test data

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

#252 - Make sure all immcantation references are cited (esp. new tools)

Issue - State: closed - Opened by ggabernet over 1 year ago - 1 comment
Labels: enhancement

#251 - Define clones with dowser

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

#250 - Back to dev

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

#249 - ci container do not run on master

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

#248 - Apply review comments

Pull Request - State: closed - Opened by ggabernet over 1 year ago - 2 comments

#247 - update aws paths

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

#246 - Add remaining R scripts to EnchantR

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

#245 - Add missing module versions

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

#244 - Bump version 3.0

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

#243 - Revert AWS test SRA bucket

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

#242 - Revert workaround for Slurm Sbatch file too large when possible

Issue - State: closed - Opened by ssnn-airr over 1 year ago - 1 comment
Labels: enhancement

#241 - Filter out sequences with NA in v_call, d_call and j_call

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

#240 - add full tests sra bucket paths

Pull Request - State: closed - Opened by ggabernet over 1 year ago - 3 comments

#239 - more changes for slurm size limit

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

#238 - Release 3.0

Pull Request - State: closed - Opened by ggabernet over 1 year ago - 3 comments

#237 - Update to EnchantR 0.1.1

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

#236 - Update EnchantR build

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

#235 - Fix Airrflow report

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

#234 - update enchantr

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

#233 - Dev

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

#232 - Clone tables after `define clone` process only contain `IGH` - `TRB` clones

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

#231 - try fix error problem pandoc

Pull Request - State: closed - Opened by ggabernet over 1 year ago - 2 comments

#230 - Add metada should add only metadata columns needed for the analyses

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

#229 - renamed enchantr argument

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

#228 - Improve docs

Pull Request - State: closed - Opened by ggabernet over 1 year ago - 2 comments

#227 - Update to `enchantR` 0.1.1

Pull Request - State: closed - Opened by ggabernet over 1 year ago - 2 comments

#226 - added crossby

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

#225 - add plotly interactive report

Pull Request - State: closed - Opened by ggabernet over 1 year ago - 2 comments

#224 - Template update v2.7.2

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

#223 - Singularity bugfix: keep report log file list in local workdir

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

#222 - Update docs and containers

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

#221 - issue #220 and docs

Pull Request - State: closed - Opened by ssnn-airr almost 2 years ago - 3 comments

#220 - Add info on README.md

Issue - State: closed - Opened by ggabernet almost 2 years ago
Labels: enhancement

#219 - Update enchantr to 0.0.6

Pull Request - State: closed - Opened by ggabernet almost 2 years ago - 2 comments

#218 - Airrflow

Pull Request - State: closed - Opened by ssnn-airr almost 2 years ago - 1 comment

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

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

#216 - Airrflow

Pull Request - State: closed - Opened by ssnn-airr almost 2 years ago - 1 comment

#215 - Template update for nf-core/tools version 2.7.1

Pull Request - State: closed - Opened by ggabernet almost 2 years ago - 1 comment

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

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

#213 - Merge template update

Pull Request - State: closed - Opened by ggabernet almost 2 years ago - 1 comment

#212 - Bump versions for 2.4.0 release

Pull Request - State: closed - Opened by ggabernet almost 2 years ago - 2 comments

#211 - PR for release 2.4.0

Pull Request - State: closed - Opened by ggabernet almost 2 years ago - 2 comments

#210 - add fastp

Pull Request - State: closed - Opened by ggabernet almost 2 years ago - 1 comment

#209 - Merge template updates nf-core v2.6

Pull Request - State: closed - Opened by ggabernet almost 2 years ago - 1 comment

#208 - Update to enchantr version 0.0.5

Pull Request - State: closed - Opened by ggabernet almost 2 years ago - 1 comment

#207 - Airrflow

Pull Request - State: closed - Opened by ssnn-airr almost 2 years ago - 2 comments

#206 - Fix input file bug

Pull Request - State: closed - Opened by ggabernet almost 2 years ago

#205 - New changes towards Enchantr 0.0.5

Pull Request - State: closed - Opened by ggabernet almost 2 years ago - 2 comments

#204 - Check where `subject_id` is converted to `null`

Issue - State: closed - Opened by ggabernet almost 2 years ago - 1 comment
Labels: bug

#203 - Enchantr report outputs

Issue - State: closed - Opened by ggabernet almost 2 years ago
Labels: enhancement

#202 - Add assembled samplesheet usage docs

Issue - State: closed - Opened by ggabernet almost 2 years ago
Labels: enhancement

#201 - Fastq samplesheet auto single_cell FALSE

Issue - State: closed - Opened by ggabernet almost 2 years ago - 1 comment
Labels: enhancement

GitHub / nf-core/airrflow issues and pull requests